Python installation problem

francicco commented 2 years ago

Hi,

I'm having this type of error during the libraries installation:

(venv) [ cactus-bin-v2.0.3]$ pip install --upgrade .
Processing /user/work/tk19812/software/cactus-bin-v2.0.3
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.3/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/user/work/tk19812/software/cactus-bin-v2.0.3/setup.py'"'"'; __file__='"'"'/user/work/tk19812/software/cactus-bin-v2.0.3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-fpr11he1
       cwd: /user/work/tk19812/software/cactus-bin-v2.0.3/
  Complete output (13 lines):
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.7/site-packages/setuptools/__init__.py", line 19, in <module>
      from setuptools.dist import Distribution
    File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.7/site-packages/_virtualenv.py", line 74, in exec_module
      old(module)
    File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.7/site-packages/setuptools/dist.py", line 38, in <module>
      from setuptools import windows_support
    File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.7/site-packages/setuptools/windows_support.py", line 2, in <module>
      import ctypes
    File "/user/home/tk19812/software/Python-3.7.6/lib/python3.7/ctypes/__init__.py", line 7, in <module>
      from _ctypes import Union, Structure, Array
  ModuleNotFoundError: No module named '_ctypes'
  ----------------------------------------
WARNING: Discarding file:///user/work/tk19812/software/cactus-bin-v2.0.3. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I don't quite understand why. Cheers F

glennhickey commented 2 years ago

Tough to say from here -- if you're on Ubuntu, you might try sudo apt-get install python3-dev

diekhans commented 2 years ago

It seems your version of python does not have ctypes compiled in.

Try: python -c 'import ctypes'

Also note the new "Cactus Release 2.0.4"

File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.7/site-packages/setuptools/windows_support.py", line 2, in <module>
  import ctypes
File "/user/home/tk19812/software/Python-3.7.6/lib/python3.7/ctypes/__init__.py", line 7, in <module>
  from _ctypes import Union, Structure, Array

ModuleNotFoundError: No module named '_ctypes'

francicco commented 2 years ago

I've now installed it, but it still gives me the same problem:

Log from job "'CactusConsolidated' kind-CactusConsolidated/instance-2pa3x_f2 v6" follows:
=========>
    [2021-11-13T18:44:01+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
    [2021-11-13T18:44:01+0000] [MainThread] [I] [toil] Running Toil version 5.5.0-b0ff5be051f2fd55352e00450b7848dcf8354a3b on host bp1-login01.data.bp.acrc.priv.
    [2021-11-13T18:44:01+0000] [MainThread] [I] [toil.worker] Working on job 'CactusConsolidated' kind-CactusConsolidated/instance-2pa3x_f2 v4
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil.worker] Loaded body Job('CactusConsolidated' kind-CactusConsolidated/instance-2pa3x_f2 v4) from description 'CactusConsolidated' kind-CactusConsolidated/instance-2pa3x_f2 v4
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil.statsAndLogging] Alignments file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmplu64x557.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [W] [root] Deprecated toil method.  Please call "logging.getLevelName" directly.
    [2021-11-13T18:44:02+0000] [MainThread] [I] [cactus.shared.common] Running the command ['cactus_consolidated', '--sequences', 'simCow_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp simDog_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp simHuman_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp simMouse_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp simRat_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp', '--speciesTree', '((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;', '--logLevel', 'INFO', '--alignments', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmplu64x557.tmp', '--params', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpfs1brh1p.tmp', '--outputFile', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpe9pwihor.tmp', '--outputHalFastaFile', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpnx1ouj8j.tmp', '--outputReferenceFile', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpn06rayek.tmp', '--outgroupEvents', 'simHuman_chr6 simMouse_chr6 simRat_chr6', '--referenceEvent', 'Anc2', '--secondaryAlignments', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp23tdvdiz.tmp', '--threads', '48']
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] 2021-11-13 18:44:02.164079: Running the command: "cactus_consolidated --sequences simCow_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp simDog_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp simHuman_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp simMouse_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp simRat_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp --speciesTree ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0; --logLevel INFO --alignments /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmplu64x557.tmp --params /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpfs1brh1p.tmp --outputFile /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpe9pwihor.tmp --outputHalFastaFile /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpnx1ouj8j.tmp --outputReferenceFile /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpn06rayek.tmp --outgroupEvents simHuman_chr6 simMouse_chr6 simRat_chr6 --referenceEvent Anc2 --secondaryAlignments /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp23tdvdiz.tmp --threads 48"
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Params file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpfs1brh1p.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Output file string : /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpe9pwihor.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Output hal fasta file string : /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpnx1ouj8j.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Output reference fasta file string : /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpn06rayek.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Sequence files and events: simCow_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp simDog_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp simHuman_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp simMouse_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp simRat_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Alignments file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmplu64x557.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Secondary alignments file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp23tdvdiz.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Constraint alignments file: (null)
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Species tree: ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Outgroup events: simHuman_chr6 simMouse_chr6 simRat_chr6
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Reference event: Anc2
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Loaded the parameters files, 0 seconds have elapsed
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Set up the cactus disk, 0 seconds have elapsed
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Constructed the first flower
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Going to build the event tree with newick string: ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Parsed the tree
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Constructed the basic event tree
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Assigning sequence /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp to simCow_chr6
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Processing file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): The file /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp is specified incomplete, the sequences will not be attached
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Assigning sequence /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp to simDog_chr6
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Processing file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): The file /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp is specified incomplete, the sequences will not be attached
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Assigning sequence /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp to simHuman_chr6
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Processing file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): The file /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp is specified incomplete, the sequences will not be attached
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Assigning sequence /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp to simMouse_chr6
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Processing file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): The file /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp is specified incomplete, the sequences will not be attached
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Assigning sequence /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp to simRat_chr6
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Processing file: /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): The file /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp is specified incomplete, the sequences will not be attached
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Constructed the initial flower with 20 sequences and 10 events with string: (((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0:9.22337e+18)ROOT:9.22337e+18;
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Established the first Flower in the hierarchy, 0 seconds have elapsed
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Converted alignment coordinates, 0 seconds have elapsed
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Stripped the unique IDs, 0 seconds have elapsed
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): There were 56884 blocks in the sequence graph, representing 1497271 total aligned bases
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Block degree stats: min 1, avg 2.900341, median 3, max 2538
    [2021-11-13T18:44:02+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Block support stats: min 0.000000, avg 0.903247, median 0.750000, max 2.000000
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Ran cactus caf, 4 seconds have elapsed
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): Ran extended flowers ready for bar, 4 seconds have elapsed
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): cactus_consolidated[0x456cce]
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): cactus_consolidated[0x44ef57]
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): cactus_consolidated[0x40f5b8]
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): cactus_consolidated[0x403c3b]
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f81d52c2555]
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): cactus_consolidated[0x403e2f]
    [2021-11-13T18:44:06+0000] [MainThread] [I] [toil-rt] cactus_consolidated(Anc2): ERROR: ERROR: Failed to get attribute: spanningTrees from cactus XML
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-mlhg237x/cleanup/file-9680357be7f34d8ca5958943dc5b6fdd/tmp0vbllzpr.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp'
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-CactusBlastPhase/instance-mlhg237x/cleanup/file-619a43c3fbf14635b5f5edcbb3163093/tmppm8_gcqd.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp'
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-TrimAndRecurseOnOutgroups/instance-3nogjsb7/file-8d583ab59bca4506be735d4ad62cd274/tmprnme3yuz.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp'
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-TrimAndRecurseOnOutgroups/instance-iyb930pj/file-52dfd06752474adda50b85a35ef01710/tmp5t_6p9gq.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp'
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-TrimAndRecurseOnOutgroups/instance-ybeblvj9/file-6e90e975685042618b47ca51da47362a/tmppkghxgcw.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp'
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-JobFunctionWrappingJob/instance-u57bbc86/file-1ea5782a379a4127acca512a2911aa94/tmpxvbmshtv.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmplu64x557.tmp'
    [2021-11-13T18:44:06+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-JobFunctionWrappingJob/instance-u57bbc86/file-c7dccf097248450da944aea1154ee0a6/tmpzj_6fuwq.tmp' to path '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp23tdvdiz.tmp'
    Traceback (most recent call last):
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/toil/worker.py", line 402, in workerScript
        job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 932, in _runner
        super(RoundedJob, self)._runner(*args, jobStore=jobStore,
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/toil/job.py", line 2362, in _runner
        returnValues = self._run(jobGraph=None, fileStore=fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/toil/job.py", line 2283, in _run
        return self.run(fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/cactus/pipeline/cactus_workflow.py", line 408, in run
        messages = runCactusConsolidated(seqMap=seqMap,
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 197, in runCactusConsolidated
        masterMessages = cactus_call(check_output=True, returnStdErr=True, realtimeStderrPrefix='cactus_consolidated({})'.format(referenceEvent),
      File "/user/work/tk19812/software/cactus-bin-v2.0.3/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 866, in cactus_call
        raise RuntimeError("Command {} exited {}: {}".format(call, process.returncode, out))
    RuntimeError: Command ['cactus_consolidated', '--sequences', 'simCow_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp276wba9e.tmp simDog_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmptxbrm80v.tmp simHuman_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp9_ma6ek4.tmp simMouse_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpaa0ky4d2.tmp simRat_chr6 /tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpt9xll15j.tmp', '--speciesTree', '((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0;', '--logLevel', 'INFO', '--alignments', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmplu64x557.tmp', '--params', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpfs1brh1p.tmp', '--outputFile', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpe9pwihor.tmp', '--outputHalFastaFile', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpnx1ouj8j.tmp', '--outputReferenceFile', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmpn06rayek.tmp', '--outgroupEvents', 'simHuman_chr6 simMouse_chr6 simRat_chr6', '--referenceEvent', 'Anc2', '--secondaryAlignments', '/tmp/651fa1d219485c38b798585adf37a59d/aff3/96f5/tmp23tdvdiz.tmp', '--threads', '48'] exited 1: stdout=A melting round is destroying 5074 blocks with an average degree of 3.686244 from chains with length less than 2. Total aligned bases lost: 18704
    A melting round is destroying 6687 blocks with an average degree of 3.045461 from chains with length less than 4. Total aligned bases lost: 45642
    A melting round is destroying 11684 blocks with an average degree of 2.394813 from chains with length less than 8. Total aligned bases lost: 140938
    A melting round is destroying 8968 blocks with an average degree of 2.420830 from chains with length less than 64. Total aligned bases lost: 224504
    Destroying 848 recoverable blocks
    The blocks covered 18849 columns for a total of 38041 aligned bases
    Destroying 0 recoverable blocks
    The blocks covered 0 columns for a total of 0 aligned bases
    , stderr=None
    [2021-11-13T18:44:06+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host bp1-login01.data.bp.acrc.priv
<=========

glennhickey commented 2 years ago

The only way I could see ERROR: ERROR: Failed to get attribute: spanningTrees from cactus XML if the configuration file Cactus is reading (passed with --configFile or read from src/cactus/cactus_progressive_config.xml) is incorrect. For example, mixing a config from version < 2.0.0 with a cactus version >= 2.0.0 would give this error.

I'd recommend removing all previous versions of cactus from your PATH and python PATH environments, dowloading and installing from scratch, and exactly following the the instructions in BIN-INSTALL.md. The fact that your log refers to Toil 5.5 and Cactus 2.0.3 is a pretty string indication to me that you haven't done this...

francicco commented 2 years ago

I'm so sorry to bother you all the time, I just realised cactus send these errors at the beginning:

=========>
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil] Running Toil version 5.5.0-b0ff5be051f2fd55352e00450b7848dcf8354a3b on host bp1-compute194.data.bp.acrc.priv.
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil.worker] Working on job 'LastzRepeatMaskJob' kind-LastzRepeatMaskJob/instance-xdi7tyda v1
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil.worker] Loaded body Job('LastzRepeatMaskJob' kind-LastzRepeatMaskJob/instance-xdi7tyda v1) from description 'LastzRepeatMaskJob' kind-LastzRepeatMaskJob/instance-xdi7tyda v1
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-f8a4208d70614e859094638cf1826447/64' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmp4rjzoeda.tmp'
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-73b409a48be244aaa09adaa9662bff21/55' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmpnqrak1w1.tmp'
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-1f0e6257df804282902f356dfaac6b3a/56' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmpxa9pco43.tmp'
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-f0ef3e1d04f74eaf8ef67011ea581846/57' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmphtlsxxhh.tmp'
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-3412263522e644f6840dbedbb6464af2/58' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmpkcxcrlq2.tmp'
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-d945ae616eea4339bb6f6bbc9d29299a/59' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmpug9m77z3.tmp'
    [2021-11-17T12:58:43+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-096a634bd64549649667412522cb36ce/60' to path '/tmp/83df1822657551d4ba3a90644bce6f80/cd1e/b6bc/tmp0y1tam0z.tmp'
    Traceback (most recent call last):
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/worker.py", line 402, in workerScript
        job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 932, in _runner
        super(RoundedJob, self)._runner(*args, jobStore=jobStore,
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/job.py", line 2362, in _runner
        returnValues = self._run(jobGraph=None, fileStore=fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/job.py", line 2283, in _run
        return self.run(fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMask.py", line 185, in run
        targetFiles = [fileStore.readGlobalFile(fileID) for fileID in self.targetIDs]
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMask.py", line 185, in <listcomp>
        targetFiles = [fileStore.readGlobalFile(fileID) for fileID in self.targetIDs]
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/fileStores/nonCachingFileStore.py", line 91, in readGlobalFile
        self.jobStore.readFile(fileStoreID, localFilePath, symlink=symlink)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/jobStores/fileJobStore.py", line 511, in readFile
        atomic_copy(jobStoreFilePath, localFilePath, executable=executable)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/lib/io.py", line 114, in atomic_copy
        shutil.copyfile(src_path, dest_path_tmp)
      File "/sw/lang/anaconda.3.8.8-2021.05/lib/python3.8/shutil.py", line 285, in copyfile
        copyfileobj(fsrc, fdst)
      File "/sw/lang/anaconda.3.8.8-2021.05/lib/python3.8/shutil.py", line 205, in copyfileobj
        buf = fsrc_read(length)
    OSError: [Errno 14] Bad address
    [2021-11-17T12:58:43+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host bp1-compute194.data.bp.acrc.priv
<=========

and this one related to memory allocation, which is very weird because it has plenty of memory to work with (700Gb), the node has (1000Gb).

=========>
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil] Running Toil version 5.5.0-b0ff5be051f2fd55352e00450b7848dcf8354a3b on host bp1-compute194.data.bp.acrc.priv.
    [2021-11-17T12:58:42+0000] [MainThread] [I] [toil.worker] Working on job 'LastzRepeatMaskJob' kind-LastzRepeatMaskJob/instance-mpajr8ud v1
    [2021-11-17T12:58:43+0000] [MainThread] [I] [toil.worker] Loaded body Job('LastzRepeatMaskJob' kind-LastzRepeatMaskJob/instance-mpajr8ud v1) from description 'LastzRepeatMaskJob' kind-LastzRepeatMaskJob/instance-mpajr8ud v1
    [2021-11-17T12:58:45+0000] [MainThread] [I] [cactus.shared.common] Running the command ['cactus_fasta_fragments.py', '--fragment=200', '--step=100', '--origin=zero']
    [2021-11-17T12:58:45+0000] [MainThread] [I] [toil-rt] 2021-11-17 12:58:45.573758: Running the command: "cactus_fasta_fragments.py --fragment=200 --step=100 --origin=zero"
    [2021-11-17T12:58:46+0000] [MainThread] [I] [toil-rt] 2021-11-17 12:58:46.048941: Successfully ran: "cactus_fasta_fragments.py --fragment=200 --step=100 --origin=zero" in 0.4654 seconds
    [2021-11-17T12:58:48+0000] [MainThread] [I] [toil-rt] 2021-11-17 12:58:48.534446: Running the command: "cPecanLastz tmp2nbhmy5n.tmp[multiple][nameparse=darkspace] tmpc6gb6uyv.tmp[nameparse=darkspace] --step=3 --ambiguous=iupac,100,100 --ungapped --queryhsplimit=keep,nowarn:1500 --querydepth=keep,nowarn:13 --format=general:name1,zstart1,end1,name2,zstart2+,end2+ --markend"
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-52c4e2a5e0234c2a9b4d71719094719f/63' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpzshi365j.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-16ee893008ee495bac13b7aa341f623b/54' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpl377h61g.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-73b409a48be244aaa09adaa9662bff21/55' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpqv88hq47.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-1f0e6257df804282902f356dfaac6b3a/56' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpswick_2s.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-f0ef3e1d04f74eaf8ef67011ea581846/57' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpaw61_5x7.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-3412263522e644f6840dbedbb6464af2/58' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpbilsivp3.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-d945ae616eea4339bb6f6bbc9d29299a/59' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpji6130z1.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-096a634bd64549649667412522cb36ce/60' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpivn8ibwe.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-0e15a725860046f3b1f8c45c4074710f/61' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmp5qoc7618.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-10a0b62fb6504db184f76d985bdac5ee/62' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpyvc_xwz4.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-52c4e2a5e0234c2a9b4d71719094719f/63' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpudrbwqbp.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-f8a4208d70614e859094638cf1826447/64' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpaid5c8zc.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-ec02dc3b7af04be18bf505ea644d2413/65' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmp2wgtgwou.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-93040aa9c4de459a83959274ae1ca7fa/66' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpdy65kzyj.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-a01cb861be0a437db616002638fd37e6/67' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpeihiu1ka.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-803cf1b61cbe4983892a82ab54dfd2a7/68' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpk8uamt2a.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-196c780ca8444e478c38c870f852c088/69' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmp834z8qv_.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-99cc2618ace849ad83984a07ac37d1f6/70' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmpg6l9rawl.tmp'
    [2021-11-17T12:58:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-PreprocessSequence/instance-24f0nemn/cleanup/file-1e1387cb8ac54aeb82ec0b15d076b199/71' to path '/tmp/83df1822657551d4ba3a90644bce6f80/be75/1f38/tmp2f7ljp03.tmp'
    Traceback (most recent call last):
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/worker.py", line 402, in workerScript
        job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 932, in _runner
        super(RoundedJob, self)._runner(*args, jobStore=jobStore,
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/job.py", line 2362, in _runner
        returnValues = self._run(jobGraph=None, fileStore=fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/job.py", line 2283, in _run
        return self.run(fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMask.py", line 192, in run
        alignment = self.alignFastaFragments(fileStore, targetFiles, fragments)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMask.py", line 86, in alignFastaFragments
        cactus_call(outfile=alignment,
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 866, in cactus_call
        raise RuntimeError("Command {} exited {}: {}".format(call, process.returncode, out))
    RuntimeError: Command ['cPecanLastz', 'tmp2nbhmy5n.tmp[multiple][nameparse=darkspace]', 'tmpc6gb6uyv.tmp[nameparse=darkspace]', '--step=3', '--ambiguous=iupac,100,100', '--ungapped', '--queryhsplimit=keep,nowarn:1500', '--querydepth=keep,nowarn:13', '--format=general:name1,zstart1,end1,name2,zstart2+,end2+', '--markend'] exited 1: stdout=None, stderr=FAILURE: I/O failure for tmp2nbhmy5n.tmp (getc reported errno=12)
    file I/O error: Cannot allocate memory

    [2021-11-17T12:58:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host bp1-compute194.data.bp.acrc.priv
<=========

diekhans commented 2 years ago

This one seems to be a bug in python or a system problem

File "/sw/lang/anaconda.3.8.8-2021.05/lib/python3.8/shutil.py", line 205, in copyfileobj
  buf = fsrc_read(length)

OSError: [Errno 14] Bad address

Could you have memory limits set:

and this one related to memory allocation, which is very weird because it has plenty of memory to work with (700Gb), the node has (1000Gb).

francicco commented 2 years ago

this is the command line:

cactus 63Nymphalidae.Cactus.scOG_ML.jobStore 63Nymphalidae.Cactus.scOG_ML.conf 63Nymphalidae.Cactus.scOG_ML.hal --maxMemory 700G --workDir /tmp --binariesMode local --stats --logFile /user/work/tk19812/HeliconiniiProject/HeliconGenomeAlignmentAnnotation/63Nymphalidae.Cactus.Hmel.log --maxCores 200 --defaultMemory 700G --realTimeLogging

diekhans commented 2 years ago

Try upgrading python

On Nov 17, 2021 at 9:42 AM, <Francesco Cicconardi @.***)> wrote:

this is the command line:

cactus 63Nymphalidae.Cactus.scOG_ML.jobStore 63Nymphalidae.Cactus.scOG_ML.conf 63Nymphalidae.Cactus.scOG_ML.hal --maxMemory 700G --workDir /tmp --binariesMode local --stats --logFile /user/work/tk19812/HeliconiniiProject/HeliconGenomeAlignmentAnnotation/63Nymphalidae.Cactus.Hmel.log --maxCores 200 --defaultMemory 700G --realTimeLogging

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francicco commented 2 years ago

I'm trying with python3.10 but I have a problem linking it to the OpenSSL during the configuration F

diekhans commented 2 years ago

We can't really help, since we don't have access to your system? Do you use Conda? it should be able to install a 3.9 easily.

Is there anyone local that can help? We barely have the time to support our own software ;-)

Francesco Cicconardi @.***> writes:

I'm trying with python3.10 but I have a problem linking it to the OpenSSL during the configuration F

francicco commented 2 years ago

I have till python3.8.8

The IT here is bloody useless F

francicco commented 2 years ago

and there's a clear conflict with the cwltool libraries. which it might be a problem from your side, I think. F

francicco commented 2 years ago

if I do:

pip install --upgrade -r toil-requirement.txt

it fails when trying to install cwltool. So what do is:

pip install cwltool==3.1.20210922203925
pip install toil
pip install --upgrade .

At this point the evolverMammals dataset works.

[2021-11-17T17:50:59+0000] [MainThread] [I] [toil.leader] Finished toil run successfully.

F

diekhans commented 2 years ago

copy and paste python install error messages, maybe I can help

francicco commented 2 years ago

These are the steps:

virtualenv -p python3.8.8 venv
source venv/bin/activate
pip install --upgrade setuptools pip
pip install --upgrade -r toil-requirement.txt

Collecting toil[all]==5.4.0
  Using cached toil-5.4.0-py3-none-any.whl (523 kB)
Collecting requests<3,>=2
  Using cached requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting docker==4.3.1
  Using cached docker-4.3.1-py2.py3-none-any.whl (145 kB)
Collecting addict<2.3,>=2.2.1
  Using cached addict-2.2.1-py3-none-any.whl (3.6 kB)
Collecting pyyaml<6,>=5
  Using cached PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl (662 kB)
Collecting psutil<6,>=3.0.1
  Using cached psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl (296 kB)
Collecting pytz>=2012
  Using cached pytz-2021.3-py2.py3-none-any.whl (503 kB)
Collecting dill<0.4,>=0.3.2
  Using cached dill-0.3.4-py2.py3-none-any.whl (86 kB)
Collecting enlighten<2,>=1.5.2
  Using cached enlighten-1.10.1-py2.py3-none-any.whl (53 kB)
Collecting python-dateutil
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting idna>=2
  Using cached idna-3.3-py3-none-any.whl (61 kB)
Collecting boto<3,>=2.48.0
  Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting wdlparse==0.1.0
  Using cached wdlparse-0.1.0-py3-none-any.whl (106 kB)
Collecting boto3<2,>=1.17
  Using cached boto3-1.20.7-py3-none-any.whl (131 kB)
Collecting kubernetes<13,>=12.0.1
  Using cached kubernetes-12.0.1-py2.py3-none-any.whl (1.7 MB)
Collecting apache-libcloud==2.2.1
  Using cached apache_libcloud-2.2.1-py2.py3-none-any.whl (2.9 MB)
Collecting cwltool==3.0.20201203173111
  Using cached cwltool-3.0.20201203173111-py3-none-any.whl (1.2 MB)
Collecting google-cloud-storage==1.6.0
  Using cached google_cloud_storage-1.6.0-py2.py3-none-any.whl (51 kB)
Collecting galaxy-tool-util
  Using cached galaxy_tool_util-21.9.1-py2.py3-none-any.whl (328 kB)
Collecting pycryptodome==3.5.1
  Using cached pycryptodome-3.5.1.tar.gz (6.7 MB)
  Preparing metadata (setup.py) ... done
Collecting pymesos==0.3.15
  Using cached pymesos-0.3.15.tar.gz (31 kB)
  Preparing metadata (setup.py) ... done
Collecting gcs-oauth2-boto-plugin==1.14
  Using cached gcs-oauth2-boto-plugin-1.14.tar.gz (14 kB)
  Preparing metadata (setup.py) ... done
Collecting futures<4,>=3.1.1
  Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Collecting pynacl==1.3.0
  Using cached PyNaCl-1.3.0-cp34-abi3-manylinux1_x86_64.whl (759 kB)
Requirement already satisfied: setuptools in ./venv/lib/python3.8/site-packages (from cwltool==3.0.20201203173111->toil[all]==5.4.0->-r toil-requirement.txt (line 1)) (59.1.1)
Collecting rdflib<4.3.0,>=4.2.2
  Using cached rdflib-4.2.2-py3-none-any.whl (344 kB)
Collecting prov==1.5.1
  Using cached prov-1.5.1-py2.py3-none-any.whl (426 kB)
Collecting ruamel.yaml<=0.16.5,>=0.12.4
  Using cached ruamel.yaml-0.16.5-py2.py3-none-any.whl (123 kB)
Collecting shellescape<3.5,>=3.4.1
  Using cached shellescape-3.4.1-py2.py3-none-any.whl (4.9 kB)
Collecting coloredlogs
  Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
Collecting pydot>=1.4.1
  Using cached pydot-1.4.2-py2.py3-none-any.whl (21 kB)
Collecting schema-salad<8,>=7
  Using cached schema_salad-7.1.20210611090601-py3-none-any.whl (471 kB)
Collecting mypy-extensions
  Using cached mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB)
Collecting bagit>=1.6.4
  Using cached bagit-1.8.1-py2.py3-none-any.whl (35 kB)
Collecting argcomplete
  Using cached argcomplete-1.12.3-py2.py3-none-any.whl (38 kB)
Collecting typing-extensions
  Using cached typing_extensions-4.0.0-py3-none-any.whl (22 kB)
Collecting websocket-client>=0.32.0
  Using cached websocket_client-1.2.1-py2.py3-none-any.whl (52 kB)
Collecting six>=1.4.0
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting httplib2>=0.8
  Using cached httplib2-0.20.2-py3-none-any.whl (96 kB)
Collecting oauth2client>=1.5.2
  Using cached oauth2client-4.1.3-py2.py3-none-any.whl (98 kB)
Collecting pyOpenSSL>=0.13
  Using cached pyOpenSSL-21.0.0-py2.py3-none-any.whl (55 kB)
Collecting SocksiPy-branch==1.01
  Using cached SocksiPy-branch-1.01.tar.gz (8.0 kB)
  Preparing metadata (setup.py) ... done
Collecting retry_decorator>=1.0.0
  Using cached retry_decorator-1.1.1.tar.gz (3.9 kB)
  Preparing metadata (setup.py) ... done
Collecting google-api-core<0.2.0dev,>=0.1.1
  Using cached google_api_core-0.1.4-py2.py3-none-any.whl (50 kB)
Collecting google-cloud-core<0.29dev,>=0.28.0
  Using cached google_cloud_core-0.28.1-py2.py3-none-any.whl (25 kB)
Collecting google-auth>=1.0.0
  Using cached google_auth-2.3.3-py2.py3-none-any.whl (155 kB)
Collecting google-resumable-media>=0.3.1
  Using cached google_resumable_media-2.1.0-py2.py3-none-any.whl (75 kB)
Collecting http-parser
  Using cached http-parser-0.9.0.tar.gz (167 kB)
  Preparing metadata (setup.py) ... done
Collecting kazoo
  Using cached kazoo-2.8.0-py2.py3-none-any.whl (142 kB)
Collecting cffi>=1.4.1
  Using cached cffi-1.15.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (446 kB)
Collecting antlr4-python3-runtime==4.8
  Using cached antlr4-python3-runtime-4.8.tar.gz (112 kB)
  Preparing metadata (setup.py) ... done
Collecting lxml
  Using cached lxml-4.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (6.9 MB)
Collecting networkx
  Using cached networkx-2.6.3-py3-none-any.whl (1.9 MB)
Collecting s3transfer<0.6.0,>=0.5.0
  Using cached s3transfer-0.5.0-py3-none-any.whl (79 kB)
Collecting jmespath<1.0.0,>=0.7.1
  Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB)
Collecting botocore<1.24.0,>=1.23.7
  Using cached botocore-1.23.7-py3-none-any.whl (8.1 MB)
Collecting prefixed>=0.3.2
  Using cached prefixed-0.3.2-py2.py3-none-any.whl (11 kB)
Collecting blessed>=1.17.7
  Using cached blessed-1.19.0-py2.py3-none-any.whl (57 kB)
Collecting urllib3>=1.24.2
  Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB)
Collecting certifi>=14.05.14
  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting requests-oauthlib
  Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.7-py3-none-any.whl (38 kB)
Collecting galaxy-containers
  Using cached galaxy_containers-21.9.0-py2.py3-none-any.whl (28 kB)
Collecting pydantic
  Using cached pydantic-1.8.2-cp38-cp38-manylinux2014_x86_64.whl (13.7 MB)
Collecting galaxy-util>=20.1.0.dev0
  Using cached galaxy_util-21.9.0-py2.py3-none-any.whl (125 kB)
Collecting sortedcontainers
  Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting wcwidth>=0.1.4
  Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Collecting pycparser
  Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Collecting routes
  Using cached Routes-2.5.1-py2.py3-none-any.whl (40 kB)
Collecting packaging
  Using cached packaging-21.2-py3-none-any.whl (40 kB)
Collecting docutils
  Using cached docutils-0.18-py2.py3-none-any.whl (569 kB)
Collecting zipstream-new
  Using cached zipstream_new-1.1.8-py3-none-any.whl (20 kB)
Collecting bleach
  Using cached bleach-4.1.0-py2.py3-none-any.whl (157 kB)
Collecting boltons
  Using cached boltons-21.0.0-py2.py3-none-any.whl (193 kB)
Collecting markupsafe
  Using cached MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB)
Collecting protobuf>=3.0.0
  Using cached protobuf-3.19.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
Collecting googleapis-common-protos<2.0dev,>=1.5.3
  Using cached googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
Collecting google-auth>=1.0.0
  Using cached google_auth-1.35.0-py2.py3-none-any.whl (152 kB)
Collecting pyasn1-modules>=0.2.1
  Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Collecting cachetools<5.0,>=2.0.0
  Using cached cachetools-4.2.4-py3-none-any.whl (10 kB)
Collecting rsa<5,>=3.1.4
  Using cached rsa-4.7.2-py3-none-any.whl (34 kB)
Collecting google-crc32c<2.0dev,>=1.0
  Using cached google_crc32c-1.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (37 kB)
Collecting pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2
  Using cached pyparsing-3.0.6-py3-none-any.whl (97 kB)
Collecting pyasn1>=0.1.7
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting cryptography>=3.3
  Using cached cryptography-35.0.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.7 MB)
Collecting isodate
  Using cached isodate-0.6.0-py2.py3-none-any.whl (45 kB)
Collecting CacheControl<0.13,>=0.11.7
  Using cached CacheControl-0.12.10-py2.py3-none-any.whl (20 kB)
Collecting rdflib-jsonld<0.6.0,>=0.3.0
  Using cached rdflib-jsonld-0.5.0.tar.gz (55 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-o_r8y46p
       cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/
  Complete output (1 lines):
  error in rdflib-jsonld setup command: use_2to3 is invalid.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/f5/17/45e137be0d93b70827fe5529c0400731344a978bc792193d7d9152e6dbe4/rdflib-jsonld-0.5.0.tar.gz#sha256=4f7d55326405071c7bce9acf5484643bcb984eadb84a6503053367da207105ed (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Using cached rdflib-jsonld-0.4.0.tar.gz (53 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/setup.py'"'"'; __file__='"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-rdxf62tr
       cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/
  Complete output (1 lines):
  error in rdflib-jsonld setup command: use_2to3 is invalid.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/ba/48/edaad22fc9de34500699f0c7fc9124385dd425fd18857244f126a6f7df66/rdflib-jsonld-0.4.0.tar.gz#sha256=144774786a2fc7de09b24a9309cbcccc78bc48b152536d2ea1c1df2ad715bc2d (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Using cached rdflib-jsonld-0.3.tar.gz (57 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/setup.py'"'"'; __file__='"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-85p4g6ht
       cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/
  Complete output (313 lines):
  creating build
  creating build/src
  creating build/src/docs
  creating build/src/rdflib_jsonld
  creating build/src/test
  creating build/src/test/test-suite
  creating build/src/test/test-suite/tests
  copying README.md -> build/src
  copying rdflib_jsonld/__init__.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/context.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/keys.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/parser.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/serializer.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/util.py -> build/src/rdflib_jsonld
  copying setup.cfg -> build/src
  copying setup.py -> build/src
  copying docs/conf.py -> build/src/docs
  copying docs/index.rst -> build/src/docs
  copying docs/jsonld-parser.rst -> build/src/docs
  copying docs/jsonld-serializer.rst -> build/src/docs
  copying docs/make.bat -> build/src/docs
  copying docs/Makefile -> build/src/docs
  copying test/.DS_Store -> build/src/test
  copying test/__init__.py -> build/src/test
  copying test/__init__.pyc -> build/src/test
  copying test/earl-context.jsonld -> build/src/test
  copying test/README.md -> build/src/test
  copying test/test_api.py -> build/src/test
  copying test/test_api.pyc -> build/src/test
  copying test/test_compaction.py -> build/src/test
  copying test/test_compaction.pyc -> build/src/test
  copying test/test_context.rst -> build/src/test
  copying test/test_testsuite.py -> build/src/test
  copying test/test_testsuite.pyc -> build/src/test
  copying test/test-suite/.DS_Store -> build/src/test/test-suite
  copying test/test-suite/context.jsonld -> build/src/test/test-suite
  copying test/test-suite/manifest.jsonld -> build/src/test/test-suite
  copying test/test-suite/README -> build/src/test/test-suite
  copying test/test-suite/vocab.jsonld -> build/src/test/test-suite
  copying test/test-suite/vocab_context.jsonld -> build/src/test/test-suite
  copying test/test-suite/tests/fromRdf-0001-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0001-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0002-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0002-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0003-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0003-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0004-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0004-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0005-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0005-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0006-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0006-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0007-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0007-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0008-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0008-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0009-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0009-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0010-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0010-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0011-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0011-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0012-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0012-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0013-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0013-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0014-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0014-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0015-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0015-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0016-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0016-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0017-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0017-out.jsonld -> build/src/test/test-suite/tests
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  copying test/test-suite/tests/toRdf-0117-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0118-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0118-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0119-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0119-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-manifest.jsonld -> build/src/test/test-suite/tests
  Skipping optional fixer: buffer
  Skipping optional fixer: idioms
  Skipping optional fixer: set_literal
  Skipping optional fixer: ws_comma
  error in rdflib-jsonld setup command: use_2to3 is invalid.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/c0/eb/f2113006f73f6270fdb29eca74ce3e6c7a172c9166aa2a482f039cda2c3e/rdflib-jsonld-0.3.tar.gz#sha256=944a1cf22a217bd78acacc183ea329848cba3f24d0cfb86541b42732cd412a88 (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Collecting schema-salad<8,>=7
  Using cached schema_salad-7.1.20210518142926-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.4 MB)
  Using cached schema_salad-7.1.20210316164414-cp38-cp38-manylinux2014_x86_64.whl (2.4 MB)
  Using cached schema_salad-7.1.20210309094900-py3-none-any.whl (471 kB)
  Using cached schema_salad-7.0.20210124093443-py3-none-any.whl (469 kB)
  Using cached schema_salad-7.0.20201119201711-py3-none-any.whl (468 kB)
  Using cached schema_salad-7.0.20200811075006-py3-none-any.whl (460 kB)
  Using cached schema_salad-7.0.20200612160654-py3-none-any.whl (459 kB)
INFO: pip is looking at multiple versions of s3transfer to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of ruamel-yaml to determine which version is compatible with other requirements. This could take a while.
Collecting ruamel.yaml<=0.16.5,>=0.12.4
  Using cached ruamel.yaml-0.16.4-py2.py3-none-any.whl (123 kB)
INFO: pip is looking at multiple versions of retry-decorator to determine which version is compatible with other requirements. This could take a while.
Collecting retry_decorator>=1.0.0
  Using cached retry_decorator-1.1.0.tar.gz (3.3 kB)
  Preparing metadata (setup.py) ... done
INFO: pip is looking at multiple versions of rdflib to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of pyopenssl to determine which version is compatible with other requirements. This could take a while.
Collecting pyOpenSSL>=0.13
  Using cached pyOpenSSL-20.0.1-py2.py3-none-any.whl (54 kB)
INFO: pip is looking at multiple versions of pydot to determine which version is compatible with other requirements. This could take a while.
Collecting pydot>=1.4.1
  Using cached pydot-1.4.1-py2.py3-none-any.whl (19 kB)
INFO: pip is looking at multiple versions of prefixed to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of oauth2client to determine which version is compatible with other requirements. This could take a while.
Collecting oauth2client>=1.5.2
  Using cached oauth2client-4.1.2-py2.py3-none-any.whl (99 kB)
INFO: pip is looking at multiple versions of jmespath to determine which version is compatible with other requirements. This could take a while.
Collecting jmespath<1.0.0,>=0.7.1
  Using cached jmespath-0.9.5-py2.py3-none-any.whl (24 kB)
INFO: pip is looking at multiple versions of httplib2 to determine which version is compatible with other requirements. This could take a while.
Collecting httplib2>=0.8
  Using cached httplib2-0.20.1-py3-none-any.whl (96 kB)
INFO: pip is looking at multiple versions of google-resumable-media to determine which version is compatible with other requirements. This could take a while.
Collecting google-resumable-media>=0.3.1
  Using cached google_resumable_media-2.0.3-py2.py3-none-any.whl (75 kB)
INFO: pip is looking at multiple versions of google-cloud-core to determine which version is compatible with other requirements. This could take a while.
Collecting google-cloud-core<0.29dev,>=0.28.0
  Using cached google_cloud_core-0.28.0-py2.py3-none-any.whl (24 kB)
INFO: pip is looking at multiple versions of google-auth to determine which version is compatible with other requirements. This could take a while.
Collecting google-auth>=1.0.0
  Using cached google_auth-1.34.0-py2.py3-none-any.whl (152 kB)
INFO: pip is looking at multiple versions of google-api-core to determine which version is compatible with other requirements. This could take a while.
Collecting google-api-core<0.2.0dev,>=0.1.1
  Using cached google_api_core-0.1.3-py2.py3-none-any.whl (49 kB)
INFO: pip is looking at multiple versions of galaxy-util to determine which version is compatible with other requirements. This could take a while.
Collecting galaxy-util>=20.1.0.dev0
  Using cached galaxy_util-21.1.0-py2.py3-none-any.whl (124 kB)
INFO: pip is looking at multiple versions of charset-normalizer to determine which version is compatible with other requirements. This could take a while.
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.6-py3-none-any.whl (37 kB)
INFO: pip is looking at multiple versions of cffi to determine which version is compatible with other requirements. This could take a while.
Collecting cffi>=1.4.1
  Using cached cffi-1.14.6-cp38-cp38-manylinux1_x86_64.whl (411 kB)
INFO: pip is looking at multiple versions of certifi to determine which version is compatible with other requirements. This could take a while.
Collecting certifi>=14.05.14
  Using cached certifi-2021.5.30-py2.py3-none-any.whl (145 kB)
INFO: pip is looking at multiple versions of botocore to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of blessed to determine which version is compatible with other requirements. This could take a while.
Collecting blessed>=1.17.7
  Using cached blessed-1.18.1-py2.py3-none-any.whl (56 kB)
INFO: pip is looking at multiple versions of bagit to determine which version is compatible with other requirements. This could take a while.
Collecting bagit>=1.6.4
  Using cached bagit-1.8.0-py2.py3-none-any.whl (35 kB)
INFO: pip is looking at multiple versions of toil to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of galaxy-tool-util to determine which version is compatible with other requirements. This could take a while.
Collecting galaxy-tool-util
  Using cached galaxy_tool_util-21.9.0-py2.py3-none-any.whl (328 kB)
INFO: pip is looking at multiple versions of requests to determine which version is compatible with other requirements. This could take a while.
Collecting requests<3,>=2
  Using cached requests-2.25.1-py2.py3-none-any.whl (61 kB)
INFO: pip is looking at multiple versions of pyyaml to determine which version is compatible with other requirements. This could take a while.
Collecting pyyaml<6,>=5
  Using cached PyYAML-5.4-cp38-cp38-manylinux1_x86_64.whl (662 kB)
INFO: pip is looking at multiple versions of pytz to determine which version is compatible with other requirements. This could take a while.
Collecting pytz>=2012
  Using cached pytz-2021.1-py2.py3-none-any.whl (510 kB)
INFO: pip is looking at multiple versions of python-dateutil to determine which version is compatible with other requirements. This could take a while.
Collecting python-dateutil
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
INFO: pip is looking at multiple versions of psutil to determine which version is compatible with other requirements. This could take a while.
Collecting psutil<6,>=3.0.1
  Using cached psutil-5.7.3.tar.gz (465 kB)
  Preparing metadata (setup.py) ... done
INFO: pip is looking at multiple versions of kubernetes to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of idna to determine which version is compatible with other requirements. This could take a while.
Collecting idna>=2
  Using cached idna-3.2-py3-none-any.whl (59 kB)
INFO: pip is looking at multiple versions of futures to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of enlighten to determine which version is compatible with other requirements. This could take a while.
Collecting enlighten<2,>=1.5.2
  Using cached enlighten-1.10.0-py2.py3-none-any.whl (53 kB)
INFO: pip is looking at multiple versions of dill to determine which version is compatible with other requirements. This could take a while.
Collecting dill<0.4,>=0.3.2
  Using cached dill-0.3.3-py2.py3-none-any.whl (81 kB)
INFO: pip is looking at multiple versions of boto3 to determine which version is compatible with other requirements. This could take a while.
Collecting boto3<2,>=1.17
  Using cached boto3-1.20.6-py3-none-any.whl (131 kB)
INFO: pip is looking at multiple versions of boto to determine which version is compatible with other requirements. This could take a while.
Collecting boto<3,>=2.48.0
  Using cached boto-2.48.0-py2.py3-none-any.whl (1.4 MB)
INFO: pip is looking at multiple versions of addict to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of socksipy-branch to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of prov to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of antlr4-python3-runtime to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of wdlparse to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of pynacl to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of pymesos to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of pycryptodome to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of google-cloud-storage to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of gcs-oauth2-boto-plugin to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of docker to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of cwltool to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of apache-libcloud to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of toil[all] to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install cwltool because these package versions have conflicting dependencies.

The conflict is caused by:
    schema-salad 7.1.20210611090601 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.1.20210518142926 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.1.20210316164414 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.1.20210309094900 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20210124093443 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20201119201711 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20200811075006 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20200612160654 depends on rdflib-jsonld<0.6.0 and >=0.3.0

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies

diekhans commented 2 years ago

please ask on the toil github ;-)

Francesco Cicconardi @.***> writes:

These are the steps:

virtualenv -p python3.8.8 venv
source venv/bin/activate
pip install --upgrade setuptools pip
pip install --upgrade -r toil-requirement.txt

Collecting toil[all]==5.4.0
  Using cached toil-5.4.0-py3-none-any.whl (523 kB)
Collecting requests<3,>=2
  Using cached requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting docker==4.3.1
  Using cached docker-4.3.1-py2.py3-none-any.whl (145 kB)
Collecting addict<2.3,>=2.2.1
  Using cached addict-2.2.1-py3-none-any.whl (3.6 kB)
Collecting pyyaml<6,>=5
  Using cached PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl (662 kB)
Collecting psutil<6,>=3.0.1
  Using cached psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl (296 kB)
Collecting pytz>=2012
  Using cached pytz-2021.3-py2.py3-none-any.whl (503 kB)
Collecting dill<0.4,>=0.3.2
  Using cached dill-0.3.4-py2.py3-none-any.whl (86 kB)
Collecting enlighten<2,>=1.5.2
  Using cached enlighten-1.10.1-py2.py3-none-any.whl (53 kB)
Collecting python-dateutil
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting idna>=2
  Using cached idna-3.3-py3-none-any.whl (61 kB)
Collecting boto<3,>=2.48.0
  Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting wdlparse==0.1.0
  Using cached wdlparse-0.1.0-py3-none-any.whl (106 kB)
Collecting boto3<2,>=1.17
  Using cached boto3-1.20.7-py3-none-any.whl (131 kB)
Collecting kubernetes<13,>=12.0.1
  Using cached kubernetes-12.0.1-py2.py3-none-any.whl (1.7 MB)
Collecting apache-libcloud==2.2.1
  Using cached apache_libcloud-2.2.1-py2.py3-none-any.whl (2.9 MB)
Collecting cwltool==3.0.20201203173111
  Using cached cwltool-3.0.20201203173111-py3-none-any.whl (1.2 MB)
Collecting google-cloud-storage==1.6.0
  Using cached google_cloud_storage-1.6.0-py2.py3-none-any.whl (51 kB)
Collecting galaxy-tool-util
  Using cached galaxy_tool_util-21.9.1-py2.py3-none-any.whl (328 kB)
Collecting pycryptodome==3.5.1
  Using cached pycryptodome-3.5.1.tar.gz (6.7 MB)
  Preparing metadata (setup.py) ... done
Collecting pymesos==0.3.15
  Using cached pymesos-0.3.15.tar.gz (31 kB)
  Preparing metadata (setup.py) ... done
Collecting gcs-oauth2-boto-plugin==1.14
  Using cached gcs-oauth2-boto-plugin-1.14.tar.gz (14 kB)
  Preparing metadata (setup.py) ... done
Collecting futures<4,>=3.1.1
  Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Collecting pynacl==1.3.0
  Using cached PyNaCl-1.3.0-cp34-abi3-manylinux1_x86_64.whl (759 kB)
Requirement already satisfied: setuptools in ./venv/lib/python3.8/site-packages (from cwltool==3.0.20201203173111->toil[all]==5.4.0->-r toil-requirement.txt (line 1)) (59.1.1)
Collecting rdflib<4.3.0,>=4.2.2
  Using cached rdflib-4.2.2-py3-none-any.whl (344 kB)
Collecting prov==1.5.1
  Using cached prov-1.5.1-py2.py3-none-any.whl (426 kB)
Collecting ruamel.yaml<=0.16.5,>=0.12.4
  Using cached ruamel.yaml-0.16.5-py2.py3-none-any.whl (123 kB)
Collecting shellescape<3.5,>=3.4.1
  Using cached shellescape-3.4.1-py2.py3-none-any.whl (4.9 kB)
Collecting coloredlogs
  Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
Collecting pydot>=1.4.1
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Collecting schema-salad<8,>=7
  Using cached schema_salad-7.1.20210611090601-py3-none-any.whl (471 kB)
Collecting mypy-extensions
  Using cached mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB)
Collecting bagit>=1.6.4
  Using cached bagit-1.8.1-py2.py3-none-any.whl (35 kB)
Collecting argcomplete
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Collecting typing-extensions
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Collecting websocket-client>=0.32.0
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Collecting six>=1.4.0
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting httplib2>=0.8
  Using cached httplib2-0.20.2-py3-none-any.whl (96 kB)
Collecting oauth2client>=1.5.2
  Using cached oauth2client-4.1.3-py2.py3-none-any.whl (98 kB)
Collecting pyOpenSSL>=0.13
  Using cached pyOpenSSL-21.0.0-py2.py3-none-any.whl (55 kB)
Collecting SocksiPy-branch==1.01
  Using cached SocksiPy-branch-1.01.tar.gz (8.0 kB)
  Preparing metadata (setup.py) ... done
Collecting retry_decorator>=1.0.0
  Using cached retry_decorator-1.1.1.tar.gz (3.9 kB)
  Preparing metadata (setup.py) ... done
Collecting google-api-core<0.2.0dev,>=0.1.1
  Using cached google_api_core-0.1.4-py2.py3-none-any.whl (50 kB)
Collecting google-cloud-core<0.29dev,>=0.28.0
  Using cached google_cloud_core-0.28.1-py2.py3-none-any.whl (25 kB)
Collecting google-auth>=1.0.0
  Using cached google_auth-2.3.3-py2.py3-none-any.whl (155 kB)
Collecting google-resumable-media>=0.3.1
  Using cached google_resumable_media-2.1.0-py2.py3-none-any.whl (75 kB)
Collecting http-parser
  Using cached http-parser-0.9.0.tar.gz (167 kB)
  Preparing metadata (setup.py) ... done
Collecting kazoo
  Using cached kazoo-2.8.0-py2.py3-none-any.whl (142 kB)
Collecting cffi>=1.4.1
  Using cached cffi-1.15.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (446 kB)
Collecting antlr4-python3-runtime==4.8
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  Preparing metadata (setup.py) ... done
Collecting lxml
  Using cached lxml-4.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (6.9 MB)
Collecting networkx
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Collecting s3transfer<0.6.0,>=0.5.0
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Collecting jmespath<1.0.0,>=0.7.1
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Collecting botocore<1.24.0,>=1.23.7
  Using cached botocore-1.23.7-py3-none-any.whl (8.1 MB)
Collecting prefixed>=0.3.2
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Collecting blessed>=1.17.7
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Collecting urllib3>=1.24.2
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Collecting certifi>=14.05.14
  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting requests-oauthlib
  Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.7-py3-none-any.whl (38 kB)
Collecting galaxy-containers
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Collecting pydantic
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Collecting galaxy-util>=20.1.0.dev0
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Collecting sortedcontainers
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Collecting wcwidth>=0.1.4
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Collecting routes
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Collecting packaging
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Collecting docutils
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Collecting markupsafe
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Collecting protobuf>=3.0.0
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Collecting googleapis-common-protos<2.0dev,>=1.5.3
  Using cached googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
Collecting google-auth>=1.0.0
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Collecting pyasn1-modules>=0.2.1
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Collecting cachetools<5.0,>=2.0.0
  Using cached cachetools-4.2.4-py3-none-any.whl (10 kB)
Collecting rsa<5,>=3.1.4
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Collecting google-crc32c<2.0dev,>=1.0
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Collecting pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2
  Using cached pyparsing-3.0.6-py3-none-any.whl (97 kB)
Collecting pyasn1>=0.1.7
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Collecting cryptography>=3.3
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Collecting isodate
  Using cached isodate-0.6.0-py2.py3-none-any.whl (45 kB)
Collecting CacheControl<0.13,>=0.11.7
  Using cached CacheControl-0.12.10-py2.py3-none-any.whl (20 kB)
Collecting rdflib-jsonld<0.6.0,>=0.3.0
  Using cached rdflib-jsonld-0.5.0.tar.gz (55 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-o_r8y46p
       cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/
  Complete output (1 lines):
  error in rdflib-jsonld setup command: use_2to3 is invalid.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/f5/17/45e137be0d93b70827fe5529c0400731344a978bc792193d7d9152e6dbe4/rdflib-jsonld-0.5.0.tar.gz#sha256=4f7d55326405071c7bce9acf5484643bcb984eadb84a6503053367da207105ed (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Using cached rdflib-jsonld-0.4.0.tar.gz (53 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/setup.py'"'"'; __file__='"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-rdxf62tr
       cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/
  Complete output (1 lines):
  error in rdflib-jsonld setup command: use_2to3 is invalid.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/ba/48/edaad22fc9de34500699f0c7fc9124385dd425fd18857244f126a6f7df66/rdflib-jsonld-0.4.0.tar.gz#sha256=144774786a2fc7de09b24a9309cbcccc78bc48b152536d2ea1c1df2ad715bc2d (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Using cached rdflib-jsonld-0.3.tar.gz (57 kB)
  Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/setup.py'"'"'; __file__='"'"'/tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-85p4g6ht
       cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/
  Complete output (313 lines):
  creating build
  creating build/src
  creating build/src/docs
  creating build/src/rdflib_jsonld
  creating build/src/test
  creating build/src/test/test-suite
  creating build/src/test/test-suite/tests
  copying README.md -> build/src
  copying rdflib_jsonld/__init__.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/context.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/keys.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/parser.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/serializer.py -> build/src/rdflib_jsonld
  copying rdflib_jsonld/util.py -> build/src/rdflib_jsonld
  copying setup.cfg -> build/src
  copying setup.py -> build/src
  copying docs/conf.py -> build/src/docs
  copying docs/index.rst -> build/src/docs
  copying docs/jsonld-parser.rst -> build/src/docs
  copying docs/jsonld-serializer.rst -> build/src/docs
  copying docs/make.bat -> build/src/docs
  copying docs/Makefile -> build/src/docs
  copying test/.DS_Store -> build/src/test
  copying test/__init__.py -> build/src/test
  copying test/__init__.pyc -> build/src/test
  copying test/earl-context.jsonld -> build/src/test
  copying test/README.md -> build/src/test
  copying test/test_api.py -> build/src/test
  copying test/test_api.pyc -> build/src/test
  copying test/test_compaction.py -> build/src/test
  copying test/test_compaction.pyc -> build/src/test
  copying test/test_context.rst -> build/src/test
  copying test/test_testsuite.py -> build/src/test
  copying test/test_testsuite.pyc -> build/src/test
  copying test/test-suite/.DS_Store -> build/src/test/test-suite
  copying test/test-suite/context.jsonld -> build/src/test/test-suite
  copying test/test-suite/manifest.jsonld -> build/src/test/test-suite
  copying test/test-suite/README -> build/src/test/test-suite
  copying test/test-suite/vocab.jsonld -> build/src/test/test-suite
  copying test/test-suite/vocab_context.jsonld -> build/src/test/test-suite
  copying test/test-suite/tests/fromRdf-0001-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0001-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0002-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0002-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0003-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0003-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0004-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0004-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0005-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0005-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0006-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0006-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0007-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0007-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0008-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0008-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0009-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0009-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0010-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0010-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0011-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0011-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0012-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0012-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0013-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0013-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0014-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0014-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0015-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0015-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0016-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0016-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0017-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0017-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0018-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0018-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0019-in.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-0019-out.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/fromRdf-manifest.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0001-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0001-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0002-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0002-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0003-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0003-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0004-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0004-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0005-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0005-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0006-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0006-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0007-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0007-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0008-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0008-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0009-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0009-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0010-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0010-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0011-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0011-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0012-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0012-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0013-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0013-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0014-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0014-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0015-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0015-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0016-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0016-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0017-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0017-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0018-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0018-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0019-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0019-out.nq -> build/src/test/test-suite/tests
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  copying test/test-suite/tests/toRdf-0020-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0022-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0022-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0023-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0023-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0024-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0024-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0025-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0025-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0026-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0026-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0027-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0027-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0028-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0028-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0029-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0029-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0030-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0030-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0031-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0031-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0032-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0032-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0033-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0033-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0034-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0034-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0035-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0035-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0036-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0036-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0041-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0041-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0042-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0042-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0043-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0043-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0044-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0044-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0045-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0045-out.nq -> build/src/test/test-suite/tests
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  copying test/test-suite/tests/toRdf-0049-out.nq -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0050-in.jsonld -> build/src/test/test-suite/tests
  copying test/test-suite/tests/toRdf-0050-out.nq -> build/src/test/test-suite/tests
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  copying test/test-suite/tests/toRdf-0054-out.nq -> build/src/test/test-suite/tests
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  Skipping optional fixer: buffer
  Skipping optional fixer: idioms
  Skipping optional fixer: set_literal
  Skipping optional fixer: ws_comma
  error in rdflib-jsonld setup command: use_2to3 is invalid.
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/c0/eb/f2113006f73f6270fdb29eca74ce3e6c7a172c9166aa2a482f039cda2c3e/rdflib-jsonld-0.3.tar.gz#sha256=944a1cf22a217bd78acacc183ea329848cba3f24d0cfb86541b42732cd412a88 (from https://pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Collecting schema-salad<8,>=7
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INFO: pip is looking at multiple versions of s3transfer to determine which version is compatible with other requirements. This could take a while.
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INFO: pip is looking at multiple versions of rdflib to determine which version is compatible with other requirements. This could take a while.
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Collecting pyOpenSSL>=0.13
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Collecting google-resumable-media>=0.3.1
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Collecting google-cloud-core<0.29dev,>=0.28.0
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INFO: pip is looking at multiple versions of google-auth to determine which version is compatible with other requirements. This could take a while.
Collecting google-auth>=1.0.0
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INFO: pip is looking at multiple versions of google-api-core to determine which version is compatible with other requirements. This could take a while.
Collecting google-api-core<0.2.0dev,>=0.1.1
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Collecting galaxy-util>=20.1.0.dev0
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Collecting charset-normalizer~=2.0.0
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Collecting certifi>=14.05.14
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Collecting bagit>=1.6.4
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Collecting psutil<6,>=3.0.1
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Collecting idna>=2
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Collecting enlighten<2,>=1.5.2
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Collecting dill<0.4,>=0.3.2
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Collecting boto<3,>=2.48.0
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INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of cwltool to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of apache-libcloud to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of toil[all] to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install cwltool because these package versions have conflicting dependencies.

The conflict is caused by:
    schema-salad 7.1.20210611090601 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.1.20210518142926 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.1.20210316164414 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.1.20210309094900 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20210124093443 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20201119201711 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20200811075006 depends on rdflib-jsonld<0.6.0 and >=0.3.0
    schema-salad 7.0.20200612160654 depends on rdflib-jsonld<0.6.0 and >=0.3.0

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/600#issuecomment-971830634 These are the steps: virtualenv -p python3.8.8 venv source venv/bin/activate pip install --upgrade setuptools pip pip install --upgrade -r toil-requirement.txt

Collecting toil[all]==5.4.0 Using cached toil-5.4.0-py3-none-any.whl (523 kB) Collecting requests<3,>=2 Using cached requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting docker==4.3.1 Using cached docker-4.3.1-py2.py3-none-any.whl (145 kB) Collecting addict<2.3,>=2.2.1 Using cached addict-2.2.1-py3-none-any.whl (3.6 kB) Collecting pyyaml<6,>=5 Using cached PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl (662 kB) Collecting psutil<6,>=3.0.1 Using cached psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl (296 kB) Collecting pytz>=2012 Using cached pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting dill<0.4,>=0.3.2 Using cached dill-0.3.4-py2.py3-none-any.whl (86 kB) Collecting enlighten<2,>=1.5.2 Using cached enlighten-1.10.1-py2.py3-none-any.whl (53 kB) Collecting python-dateutil Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting idna>=2 Using cached idna-3.3-py3-none-any.whl (61 kB) Collecting boto<3,>=2.48.0 Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB) Collecting wdlparse==0.1.0 Using cached wdlparse-0.1.0-py3-none-any.whl (106 kB) Collecting boto3<2,>=1.17 Using cached boto3-1.20.7-py3-none-any.whl (131 kB) Collecting kubernetes<13,>=12.0.1 Using cached kubernetes-12.0.1-py2.py3-none-any.whl (1.7 MB) Collecting apache-libcloud==2.2.1 Using cached apache_libcloud-2.2.1-py2.py3-none-any.whl (2.9 MB) Collecting cwltool==3.0.20201203173111 Using cached cwltool-3.0.20201203173111-py3-none-any.whl (1.2 MB) Collecting google-cloud-storage==1.6.0 Using cached google_cloud_storage-1.6.0-py2.py3-none-any.whl (51 kB) Collecting galaxy-tool-util Using cached galaxy_tool_util-21.9.1-py2.py3-none-any.whl (328 kB) Collecting pycryptodome==3.5.1 Using cached pycryptodome-3.5.1.tar.gz (6.7 MB) Preparing metadata (setup.py) ... done Collecting pymesos==0.3.15 Using cached pymesos-0.3.15.tar.gz (31 kB) Preparing metadata (setup.py) ... done Collecting gcs-oauth2-boto-plugin==1.14 Using cached gcs-oauth2-boto-plugin-1.14.tar.gz (14 kB) Preparing metadata (setup.py) ... done Collecting futures<4,>=3.1.1 Using cached futures-3.1.1-py3-none-any.whl (2.8 kB) Collecting pynacl==1.3.0 Using cached PyNaCl-1.3.0-cp34-abi3-manylinux1_x86_64.whl (759 kB) Requirement already satisfied: setuptools in ./venv/lib/python3.8/site-packages (from cwltool==3.0.20201203173111->toil[all]==5.4.0->-r toil-requirement.txt (li ne 1)) (59.1.1) Collecting rdflib<4.3.0,>=4.2.2 Using cached rdflib-4.2.2-py3-none-any.whl (344 kB) Collecting prov==1.5.1 Using cached prov-1.5.1-py2.py3-none-any.whl (426 kB) Collecting ruamel.yaml<=0.16.5,>=0.12.4 Using cached ruamel.yaml-0.16.5-py2.py3-none-any.whl (123 kB) Collecting shellescape<3.5,>=3.4.1 Using cached shellescape-3.4.1-py2.py3-none-any.whl (4.9 kB) Collecting coloredlogs Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) Collecting pydot>=1.4.1 Using cached pydot-1.4.2-py2.py3-none-any.whl (21 kB) Collecting schema-salad<8,>=7 Using cached schema_salad-7.1.20210611090601-py3-none-any.whl (471 kB) Collecting mypy-extensions Using cached mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB) Collecting bagit>=1.6.4 Using cached bagit-1.8.1-py2.py3-none-any.whl (35 kB) Collecting argcomplete Using cached argcomplete-1.12.3-py2.py3-none-any.whl (38 kB) Collecting typing-extensions Using cached typing_extensions-4.0.0-py3-none-any.whl (22 kB) Collecting websocket-client>=0.32.0 Using cached websocket_client-1.2.1-py2.py3-none-any.whl (52 kB) Collecting six>=1.4.0 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting httplib2>=0.8 Using cached httplib2-0.20.2-py3-none-any.whl (96 kB) Collecting oauth2client>=1.5.2 Using cached oauth2client-4.1.3-py2.py3-none-any.whl (98 kB) Collecting pyOpenSSL>=0.13 Using cached pyOpenSSL-21.0.0-py2.py3-none-any.whl (55 kB) Collecting SocksiPy-branch==1.01 Using cached SocksiPy-branch-1.01.tar.gz (8.0 kB) Preparing metadata (setup.py) ... done Collecting retry_decorator>=1.0.0 Using cached retry_decorator-1.1.1.tar.gz (3.9 kB) Preparing metadata (setup.py) ... done Collecting google-api-core<0.2.0dev,>=0.1.1 Using cached google_api_core-0.1.4-py2.py3-none-any.whl (50 kB) Collecting google-cloud-core<0.29dev,>=0.28.0 Using cached google_cloud_core-0.28.1-py2.py3-none-any.whl (25 kB) Collecting google-auth>=1.0.0 Using cached google_auth-2.3.3-py2.py3-none-any.whl (155 kB) Collecting google-resumable-media>=0.3.1 Using cached google_resumable_media-2.1.0-py2.py3-none-any.whl (75 kB) Collecting http-parser Using cached http-parser-0.9.0.tar.gz (167 kB) Preparing metadata (setup.py) ... done Collecting kazoo Using cached kazoo-2.8.0-py2.py3-none-any.whl (142 kB) Collecting cffi>=1.4.1 Using cached cffi-1.15.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64. whl (446 kB) Collecting antlr4-python3-runtime==4.8 Using cached antlr4-python3-runtime-4.8.tar.gz (112 kB) Preparing metadata (setup.py) ... done Collecting lxml Using cached lxml-4.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.m anylinux_2_24_x86_64.whl (6.9 MB) Collecting networkx Using cached networkx-2.6.3-py3-none-any.whl (1.9 MB) Collecting s3transfer<0.6.0,>=0.5.0 Using cached s3transfer-0.5.0-py3-none-any.whl (79 kB) Collecting jmespath<1.0.0,>=0.7.1 Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB) Collecting botocore<1.24.0,>=1.23.7 Using cached botocore-1.23.7-py3-none-any.whl (8.1 MB) Collecting prefixed>=0.3.2 Using cached prefixed-0.3.2-py2.py3-none-any.whl (11 kB) Collecting blessed>=1.17.7 Using cached blessed-1.19.0-py2.py3-none-any.whl (57 kB) Collecting urllib3>=1.24.2 Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting certifi>=14.05.14 Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting requests-oauthlib Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB) Collecting charset-normalizer~=2.0.0 Using cached charset_normalizer-2.0.7-py3-none-any.whl (38 kB) Collecting galaxy-containers Using cached galaxy_containers-21.9.0-py2.py3-none-any.whl (28 kB) Collecting pydantic Using cached pydantic-1.8.2-cp38-cp38-manylinux2014_x86_64.whl (13.7 MB) Collecting galaxy-util>=20.1.0.dev0 Using cached galaxy_util-21.9.0-py2.py3-none-any.whl (125 kB) Collecting sortedcontainers Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB) Collecting wcwidth>=0.1.4 Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB) Collecting pycparser Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB) Collecting routes Using cached Routes-2.5.1-py2.py3-none-any.whl (40 kB) Collecting packaging Using cached packaging-21.2-py3-none-any.whl (40 kB) Collecting docutils Using cached docutils-0.18-py2.py3-none-any.whl (569 kB) Collecting zipstream-new Using cached zipstream_new-1.1.8-py3-none-any.whl (20 kB) Collecting bleach Using cached bleach-4.1.0-py2.py3-none-any.whl (157 kB) Collecting boltons Using cached boltons-21.0.0-py2.py3-none-any.whl (193 kB) Collecting markupsafe Using cached MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64 .manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB) Collecting protobuf>=3.0.0 Using cached protobuf-3.19.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86 _64.whl (1.1 MB) Collecting googleapis-common-protos<2.0dev,>=1.5.3 Using cached googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB) Collecting google-auth>=1.0.0 Using cached google_auth-1.35.0-py2.py3-none-any.whl (152 kB) Collecting pyasn1-modules>=0.2.1 Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB) Collecting cachetools<5.0,>=2.0.0 Using cached cachetools-4.2.4-py3-none-any.whl (10 kB) Collecting rsa<5,>=3.1.4 Using cached rsa-4.7.2-py3-none-any.whl (34 kB) Collecting google-crc32c<2.0dev,>=1.0 Using cached google_crc32c-1.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010 _x86_64.whl (37 kB) Collecting pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 Using cached pyparsing-3.0.6-py3-none-any.whl (97 kB) Collecting pyasn1>=0.1.7 Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB) Collecting cryptography>=3.3 Using cached cryptography-35.0.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014 _x86_64.whl (3.7 MB) Collecting isodate Using cached isodate-0.6.0-py2.py3-none-any.whl (45 kB) Collecting CacheControl<0.13,>=0.11.7 Using cached CacheControl-0.12.10-py2.py3-none-any.whl (20 kB) Collecting rdflib-jsonld<0.6.0,>=0.3.0 Using cached rdflib-jsonld-0.5.0.tar.gz (55 kB) Preparing metadata (setup.py) ... error ERROR: Command errored out with exit status 1: command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'im port io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8zn b0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec8601dc9/setup.py'"'"'; file='"'" '/tmp/pip-install-n8znb0z7/rdflib-jsonldf17321e1a6a04b1b9a23b2bec8601dc9/setup. py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists( file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, _file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-o_r8y46p cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_f17321e1a6a04b1b9a23b2bec860 1dc9/ Complete output (1 lines): error in rdflib-jsonld setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/f5/17/45e137be0d93b7 0827fe5529c0400731344a978bc792193d7d9152e6dbe4/rdflib-jsonld-0.5.0.tar.gz#sha256 =4f7d55326405071c7bce9acf5484643bcb984eadb84a6503053367da207105ed (from https:// pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached rdflib-jsonld-0.4.0.tar.gz (53 kB) Preparing metadata (setup.py) ... error ERROR: Command errored out with exit status 1: command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'im port io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8zn b0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4fbfe/setup.py'"'"'; file='"'" '/tmp/pip-install-n8znb0z7/rdflib-jsonld71c1a50e4bef42088cb8a81b3bb4fbfe/setup. py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists( file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, _file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-rdxf62tr cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_71c1a50e4bef42088cb8a81b3bb4 fbfe/ Complete output (1 lines): error in rdflib-jsonld setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/ba/48/edaad22fc9de34 500699f0c7fc9124385dd425fd18857244f126a6f7df66/rdflib-jsonld-0.4.0.tar.gz#sha256 =144774786a2fc7de09b24a9309cbcccc78bc48b152536d2ea1c1df2ad715bc2d (from https:// pypi.org/simple/rdflib-jsonld/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached rdflib-jsonld-0.3.tar.gz (57 kB) Preparing metadata (setup.py) ... error ERROR: Command errored out with exit status 1: command: /user/work/tk19812/software/cactus-bin-v2.0.4/venv/bin/python -c 'im port io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-n8zn b0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb365ad/setup.py'"'"'; file='"'" '/tmp/pip-install-n8znb0z7/rdflib-jsonldba17a4f3b6a049dba78b0ca26cb365ad/setup. py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists( file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, _file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-85p4g6ht cwd: /tmp/pip-install-n8znb0z7/rdflib-jsonld_ba17a4f3b6a049dba78b0ca26cb3 65ad/ Complete output (313 lines): creating build creating build/src creating build/src/docs creating build/src/rdflib_jsonld creating build/src/test creating build/src/test/test-suite creating build/src/test/test-suite/tests copying README.md -> build/src copying rdflib_jsonld/init.py -> build/src/rdflib_jsonld copying rdflib_jsonld/context.py -> build/src/rdflib_jsonld copying rdflib_jsonld/keys.py -> build/src/rdflib_jsonld copying rdflib_jsonld/parser.py -> build/src/rdflib_jsonld copying rdflib_jsonld/serializer.py -> build/src/rdflib_jsonld copying rdflib_jsonld/util.py -> build/src/rdflib_jsonld copying setup.cfg -> build/src copying setup.py -> build/src copying docs/conf.py -> build/src/docs copying docs/index.rst -> build/src/docs copying docs/jsonld-parser.rst -> build/src/docs copying docs/jsonld-serializer.rst -> build/src/docs copying docs/make.bat -> build/src/docs copying docs/Makefile -> build/src/docs copying test/.DS_Store -> build/src/test copying test/init.py -> build/src/test copying test/init__.pyc -> build/src/test copying test/earl-context.jsonld -> build/src/test copying test/README.md -> build/src/test copying test/test_api.py -> build/src/test copying test/test_api.pyc -> build/s

glennhickey commented 2 years ago

Take a look here for a workaround https://github.com/ComparativeGenomicsToolkit/cactus/issues/599

francicco commented 2 years ago

Thanks a lot! The installation now didn't complain a bit, but at the moment I'm still having a the memory issue:

=========>
    [2021-11-18T10:16:24+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
    [2021-11-18T10:16:24+0000] [MainThread] [I] [toil] Running Toil version 5.4.0-87293d63fa6c76f03bed3adf93414ffee67bf9a7 on host bp1-compute194.data.bp.acrc.priv.
    [2021-11-18T10:16:24+0000] [MainThread] [I] [toil.worker] Working on job 'PreprocessSequence' kind-PreprocessSequence/instance-pcgsyff5
    [2021-11-18T10:16:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('PreprocessSequence' kind-PreprocessSequence/instance-pcgsyff5) from description 'PreprocessSequence' kind-PreprocessSequence/instance-pcgsyff5
    [2021-11-18T10:16:25+0000] [MainThread] [I] [toil.statsAndLogging] Preparing sequence for preprocessing
    Traceback (most recent call last):
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/worker.py", line 393, in workerScript
        job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 932, in _runner
        super(RoundedJob, self)._runner(*args, jobStore=jobStore,
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/job.py", line 2360, in _runner
        returnValues = self._run(jobGraph=None, fileStore=fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/job.py", line 2281, in _run
        return self.run(fileStore)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/cactus/preprocessor/cactus_preprocessor.py", line 173, in run
        inSequence = fileStore.readGlobalFile(self.inSequenceID)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/fileStores/nonCachingFileStore.py", line 91, in readGlobalFile
        self.jobStore.readFile(fileStoreID, localFilePath, symlink=symlink)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/jobStores/fileJobStore.py", line 505, in readFile
        atomic_copy(jobStoreFilePath, localFilePath, executable=executable)
      File "/user/work/tk19812/software/cactus-bin-v2.0.4/venv/lib/python3.8/site-packages/toil/lib/io.py", line 114, in atomic_copy
        shutil.copyfile(src_path, dest_path_tmp)
      File "/sw/lang/anaconda.3.8.8-2021.05/lib/python3.8/shutil.py", line 275, in copyfile
        _fastcopy_sendfile(fsrc, fdst)
      File "/sw/lang/anaconda.3.8.8-2021.05/lib/python3.8/shutil.py", line 172, in _fastcopy_sendfile
        raise err
      File "/sw/lang/anaconda.3.8.8-2021.05/lib/python3.8/shutil.py", line 152, in _fastcopy_sendfile
        sent = os.sendfile(outfd, infd, offset, blocksize)
    OSError: [Errno 12] Cannot allocate memory: '/user/work/tk19812/HeliconiniiProject/HeliconGenomeAlignmentAnnotation/63Nymphalidae.Cactus.scOG_ML.jobStore/files/no-job/file-025ae0ee76b64b96ae5582f9495b4f47/Hleu.assembly.v0.9.fasta.masked' -> '/tmp/de87a764c06b5012b67c5b4ff7476fce/8a94/e949/tmpder8zx9q.tmp.7d17d748-1b34-4d03-b4b0-121125a99251.tmp.tmp'
    [2021-11-18T10:16:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host bp1-compute194.data.bp.acrc.priv
<=========

Is that due to the cluster or python? F

francicco commented 2 years ago

It seems like I've fixed the memory part. :) Let's see what else happens! :D Thanks a lot! F

Aannaw commented 2 years ago

Hello I also met the problem when I install cactus running the command "python3 -m pip install -U -r ./toil-requirement.txt":

Collecting antlr4-python3-runtime==4.8                                                                                                                      
  Using cached antlr4-python3-runtime-4.8.tar.gz (112 kB)                                                                                      
  Preparing metadata (setup.py) ... error                                                                                                        
  ERROR: Command errored out with exit status 1:                                                                                                             
   command: /data/00/user/user157/Python39/bin/python3.9 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xtdlm8hz/antlr4-py
thon3-runtime_75c324b3d1de4dc0bb8d461ed848d63e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-xtdlm8hz/antlr4-python3-runtime_75c324b3d1de4dc0bb8d461ed848d63e
/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'
"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-inf
o-9wf87y1n                                                                                                                                                  
       cwd: /tmp/pip-install-xtdlm8hz/antlr4-python3-runtime_75c324b3d1de4dc0bb8d461ed848d63e/                
  Complete output (11 lines):                                                                                                                               
  Traceback (most recent call last):                                                                                                                     
    File "<string>", line 1, in <module>
    File "/data/00/user/user157/Python39/lib/python3.9/site-packages/setuptools/__init__.py", line 18, in <module>
      from setuptools.dist import Distribution
    File "/data/00/user/user157/Python39/lib/python3.9/site-packages/setuptools/dist.py", line 39, in <module>
      from setuptools import windows_support
    File "/data/00/user/user157/Python39/lib/python3.9/site-packages/setuptools/windows_support.py", line 2, in <module>
      import ctypes
    File "/data/00/user/user157/Python39/lib/python3.9/ctypes/__init__.py", line 8, in <module>
      from _ctypes import Union, Structure, Array
  ModuleNotFoundError: No module named '_ctypes'
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/56/02/789a0bddf9c9b31b14c3e79ec22b9656185a803dc31c15f006f9855ece0d/antlr4-python3-runtime-4.8.tar
.gz#sha256=15793f5d0512a372b4e7d2284058ad32ce7dd27126b105fb0b2245130445db33 (from https://pypi.org/simple/antlr4-python3-runtime/). Command errored out with 
exit status 1: python setup.py egg_info Check the logs for full command output.
INFO: pip is looking at multiple versions of ruamel-yaml to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of gunicorn to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of google-cloud-storage to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of flask-cors to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take
a while.
INFO: pip is looking at multiple versions of cwltool to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of toil[all] to determine which version is compatible with other requirements. This could take a while.
ERROR: Could not find a version that satisfies the requirement antlr4-python3-runtime==4.8 (from wdlparse) (from versions: 4.4.0, 4.4.1, 4.5, 4.5.2, 4.5.2.1,
 4.5.3, 4.6, 4.7, 4.7.1, 4.7.2, 4.8, 4.9, 4.9.1, 4.9.2, 4.9.3)
ERROR: No matching distribution found for antlr4-python3-runtime==4.8
WARNING: You are using pip version 21.3.1; however, version 22.0.3 is available.
You should consider upgrading via the '/data/00/user/user157/Python39/bin/python3.9 -m pip install --upgrade pip' command.

My command is:

pip3 install virtualenv
virtualenv -p python3.9 cactus
echo 'export PATH=$(pwd)/bin:$PATH' >> cactus_env/bin/activate
echo 'export PYTHONPATH=$(pwd)/lib:$PYTHONPATH' >> cactus_env/bin/activate
source cactus/bin/activate
python3 -m pip install -U setuptools pip==21.3.1
python3 -m pip install -U -r ./toil-requirement.txt

Could you give me any suggestions?

glennhickey commented 2 years ago

If you're on ubuntu, you can try sudo apt-get install libffi-dev

ComparativeGenomicsToolkit / cactus

Python installation problem #600