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smirarab / pasta

PASTA (Practical Alignment using SATe and Transitivity)
GNU General Public License v3.0
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Issues in setup.py #30

Open niemasd opened 6 years ago

niemasd commented 6 years ago

In the README, in step 5 (run sudo python setup.py develop), I think the setup.py script is expecting Python 3, because I get the following error message:

Traceback (most recent call last):
  File "setup.py", line 14, in <module>
    ez_setup.use_setuptools()
  File "/root/pasta/ez_setup.py", line 98, in use_setuptools
    return do_download()       
  File "/root/pasta/ez_setup.py", line 92, in do_download
    egg = download_setuptools(version, download_base, to_dir, download_delay)
  File "/root/pasta/ez_setup.py", line 127, in download_setuptools
    import urllib.request, urllib.error, urllib.parse, shutil
ImportError: No module named request

In Python 2, it's urllib2.request, not urllib.request, which is why I think it's expecting Python 3. I think this holds true for the other urllib things being imported too (https://docs.python.org/2/library/urllib.html). It might be good to add a version check or perhaps a try-except block, e.g.:

try: # Python 3
    import urllib.request, urllib.error, urllib.parse, shutil
except: # Python 2
    # do whatever the correct thing is in Python 2
niemasd commented 6 years ago

Now, trying Python 3 (i.e., sudo python3 setup.py develop), I get the following error:

  File "setup.py", line 200
    fullPath = os.path.join(searchDir, files)
                                            ^
TabError: inconsistent use of tabs and spaces in indentation

It seems like it might be a good idea to overall check the setup.py script

niemasd commented 6 years ago

Fixed tab/space issue: https://github.com/smirarab/pasta/commit/22e855fabb7f512d06a9173279d3293c33666e97

Haven't attempted to fix the urllib import error

niemasd commented 6 years ago

Now (in Python 3) the setup.py script starts at makes progress, but it errors out like this:

Creating link: '/usr/local/bin/pasta/resources/scripts/hmmeralign' => '/usr/local/bin/pasta/bin/hmmeralign'
Creating link: '/usr/local/bin/sate-tools-linux/randtree' => '/usr/local/bin/pasta/bin/randtree'
Creating link: '/usr/local/bin/sate-tools-linux/opal.jar' => '/usr/local/bin/pasta/bin/opal.jar'
Creating link: '/usr/local/bin/sate-tools-linux/fasttreeMP' => '/usr/local/bin/pasta/bin/fasttreeMP'
Creating link: '/usr/local/bin/sate-tools-linux/muscle' => '/usr/local/bin/pasta/bin/muscle'
Creating link: '/usr/local/bin/sate-tools-linux/fakealigner' => '/usr/local/bin/pasta/bin/fakealigner'
Creating link: '/usr/local/bin/sate-tools-linux/clustalw2' => '/usr/local/bin/pasta/bin/clustalw2'
Creating link: '/usr/local/bin/sate-tools-linux/.gitignore' => '/usr/local/bin/pasta/bin/.gitignore'
Creating link: '/usr/local/bin/sate-tools-linux/fasttree' => '/usr/local/bin/pasta/bin/fasttree'
Creating link: '/usr/local/bin/sate-tools-linux/raxml' => '/usr/local/bin/pasta/bin/raxml'
Creating link: '/usr/local/bin/sate-tools-linux/contralign' => '/usr/local/bin/pasta/bin/contralign'
Creating link: '/usr/local/bin/sate-tools-linux/mafft' => '/usr/local/bin/pasta/bin/mafft'
Creating link: '/usr/local/bin/sate-tools-linux/contralign.topology' => '/usr/local/bin/pasta/bin/contralign.topology'
Creating link: '/usr/local/bin/sate-tools-linux/raxmlp' => '/usr/local/bin/pasta/bin/raxmlp'
Creating link: '/usr/local/bin/sate-tools-linux/faketree' => '/usr/local/bin/pasta/bin/faketree'
Creating link: '/usr/local/bin/sate-tools-linux/padaligner' => '/usr/local/bin/pasta/bin/padaligner'
Creating link: '/usr/local/bin/sate-tools-linux/homologs' => '/usr/local/bin/pasta/bin/homologs'
Creating link: '/usr/local/bin/sate-tools-linux/prank' => '/usr/local/bin/pasta/bin/prank'
Creating link: '/usr/local/bin/sate-tools-linux/hmmalign' => '/usr/local/bin/pasta/bin/hmmalign'
Creating link: '/usr/local/bin/sate-tools-linux/hmmbuild' => '/usr/local/bin/pasta/bin/hmmbuild'
Creating link: '/usr/local/bin/sate-tools-linux/contralign.params' => '/usr/local/bin/pasta/bin/contralign.params'
Creating link: '/usr/local/bin/sate-tools-linux/probcons' => '/usr/local/bin/pasta/bin/probcons'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/bin/mafft' => '/usr/local/bin/pasta/bin/mafftdir/bin/mafft'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/splittbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/splittbfast'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/setcore' => '/usr/local/bin/pasta/bin/mafftdir/libexec/setcore'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndpre2' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndpre2'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pairash' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pairash'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndfast7' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndfast7'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/contrafoldwrap' => '/usr/local/bin/pasta/bin/mafftdir/libexec/contrafoldwrap'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/score' => '/usr/local/bin/pasta/bin/mafftdir/libexec/score'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/getlag' => '/usr/local/bin/pasta/bin/mafftdir/libexec/getlag'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/addsingle' => '/usr/local/bin/pasta/bin/mafftdir/libexec/addsingle'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-distance' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-distance'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/restoreu' => '/usr/local/bin/pasta/bin/mafftdir/libexec/restoreu'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/sextet5' => '/usr/local/bin/pasta/bin/mafftdir/libexec/sextet5'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/version' => '/usr/local/bin/pasta/bin/mafftdir/libexec/version'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/makedirectionlist' => '/usr/local/bin/pasta/bin/mafftdir/libexec/makedirectionlist'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/regtable2seq' => '/usr/local/bin/pasta/bin/mafftdir/libexec/regtable2seq'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft.1' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft.1'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/setdirection' => '/usr/local/bin/pasta/bin/mafftdir/libexec/setdirection'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/rnatest' => '/usr/local/bin/pasta/bin/mafftdir/libexec/rnatest'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndblast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndblast'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/seq2regtable' => '/usr/local/bin/pasta/bin/mafftdir/libexec/seq2regtable'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/replaceu' => '/usr/local/bin/pasta/bin/mafftdir/libexec/replaceu'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndpre' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndpre'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dvtditr' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dvtditr'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pairlocalalign' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pairlocalalign'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-profile' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-profile'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/multi2hat3s' => '/usr/local/bin/pasta/bin/mafftdir/libexec/multi2hat3s'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pair2hat3s' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pair2hat3s'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/tbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/tbfast'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-homologs.1' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-homologs.1'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafftash_premafft.pl' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafftash_premafft.pl'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mccaskillwrap' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mccaskillwrap'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/f2cl' => '/usr/local/bin/pasta/bin/mafftdir/libexec/f2cl'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/countlen' => '/usr/local/bin/pasta/bin/mafftdir/libexec/countlen'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/disttbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/disttbfast'
Traceback (most recent call last):
  File "setup.py", line 199, in <module>
    for files in os.listdir(searchDir):
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/sate-tools-linux/databases'

I checked the sate-tools-linux repository, and there's no databases folder, which is why this error is getting triggered. Looking at the commit history, it seems like the files in the databases folder were deleted 11 days ago. I'm not sure what these databases were used for nor how their deletion affects PASTA setup, so I won't remove these symlink lines, but someone should look into this

niemasd commented 6 years ago

I got around the sate-tools-linux symlink error for now by reverting it to commit d78ef029b533e4f4ac13ba1e9cfdac7944b1f70e before running setup.py

smirarab commented 6 years ago

Hi Kodi,

Can you take a look at this error and fix it?

Thanks Siavash

---------- Forwarded message ---------- From: Niema Moshiri notifications@github.com Date: Sun, Apr 15, 2018 at 12:21 PM Subject: Re: [smirarab/pasta] Issues in setup.py (#30) To: smirarab/pasta pasta@noreply.github.com Cc: Subscribed subscribed@noreply.github.com

Now (in Python 3) the setup.py script starts at makes progress, but it errors out like this:

Creating link: '/usr/local/bin/pasta/resources/scripts/hmmeralign' => '/usr/local/bin/pasta/bin/hmmeralign' Creating link: '/usr/local/bin/sate-tools-linux/randtree' => '/usr/local/bin/pasta/bin/randtree' Creating link: '/usr/local/bin/sate-tools-linux/opal.jar' => '/usr/local/bin/pasta/bin/opal.jar' Creating link: '/usr/local/bin/sate-tools-linux/fasttreeMP' => '/usr/local/bin/pasta/bin/fasttreeMP' Creating link: '/usr/local/bin/sate-tools-linux/muscle' => '/usr/local/bin/pasta/bin/muscle' Creating link: '/usr/local/bin/sate-tools-linux/fakealigner' => '/usr/local/bin/pasta/bin/fakealigner' Creating link: '/usr/local/bin/sate-tools-linux/clustalw2' => '/usr/local/bin/pasta/bin/clustalw2' Creating link: '/usr/local/bin/sate-tools-linux/.gitignore' => '/usr/local/bin/pasta/bin/.gitignore' Creating link: '/usr/local/bin/sate-tools-linux/fasttree' => '/usr/local/bin/pasta/bin/fasttree' Creating link: '/usr/local/bin/sate-tools-linux/raxml' => '/usr/local/bin/pasta/bin/raxml' Creating link: '/usr/local/bin/sate-tools-linux/contralign' => '/usr/local/bin/pasta/bin/contralign' Creating link: '/usr/local/bin/sate-tools-linux/mafft' => '/usr/local/bin/pasta/bin/mafft' Creating link: '/usr/local/bin/sate-tools-linux/contralign.topology' => '/usr/local/bin/pasta/bin/contralign.topology' Creating link: '/usr/local/bin/sate-tools-linux/raxmlp' => '/usr/local/bin/pasta/bin/raxmlp' Creating link: '/usr/local/bin/sate-tools-linux/faketree' => '/usr/local/bin/pasta/bin/faketree' Creating link: '/usr/local/bin/sate-tools-linux/padaligner' => '/usr/local/bin/pasta/bin/padaligner' Creating link: '/usr/local/bin/sate-tools-linux/homologs' => '/usr/local/bin/pasta/bin/homologs' Creating link: '/usr/local/bin/sate-tools-linux/prank' => '/usr/local/bin/pasta/bin/prank' Creating link: '/usr/local/bin/sate-tools-linux/hmmalign' => '/usr/local/bin/pasta/bin/hmmalign' Creating link: '/usr/local/bin/sate-tools-linux/hmmbuild' => '/usr/local/bin/pasta/bin/hmmbuild' Creating link: '/usr/local/bin/sate-tools-linux/contralign.params' => '/usr/local/bin/pasta/bin/contralign.params' Creating link: '/usr/local/bin/sate-tools-linux/probcons' => '/usr/local/bin/pasta/bin/probcons' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/bin/mafft' => '/usr/local/bin/pasta/bin/mafftdir/bin/mafft' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/splittbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/splittbfast' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/setcore' => '/usr/local/bin/pasta/bin/mafftdir/libexec/setcore' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndpre2' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndpre2' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pairash' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pairash' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndfast7' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndfast7' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/contrafoldwrap' => '/usr/local/bin/pasta/bin/mafftdir/libexec/contrafoldwrap' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/score' => '/usr/local/bin/pasta/bin/mafftdir/libexec/score' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/getlag' => '/usr/local/bin/pasta/bin/mafftdir/libexec/getlag' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/addsingle' => '/usr/local/bin/pasta/bin/mafftdir/libexec/addsingle' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-distance' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-distance' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/restoreu' => '/usr/local/bin/pasta/bin/mafftdir/libexec/restoreu' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/sextet5' => '/usr/local/bin/pasta/bin/mafftdir/libexec/sextet5' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/version' => '/usr/local/bin/pasta/bin/mafftdir/libexec/version' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/makedirectionlist' => '/usr/local/bin/pasta/bin/mafftdir/libexec/makedirectionlist' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/regtable2seq' => '/usr/local/bin/pasta/bin/mafftdir/libexec/regtable2seq' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft.1' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft.1' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/setdirection' => '/usr/local/bin/pasta/bin/mafftdir/libexec/setdirection' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/rnatest' => '/usr/local/bin/pasta/bin/mafftdir/libexec/rnatest' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndblast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndblast' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/seq2regtable' => '/usr/local/bin/pasta/bin/mafftdir/libexec/seq2regtable' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/replaceu' => '/usr/local/bin/pasta/bin/mafftdir/libexec/replaceu' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndpre' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndpre' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dvtditr' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dvtditr' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pairlocalalign' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pairlocalalign' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-profile' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-profile' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/multi2hat3s' => '/usr/local/bin/pasta/bin/mafftdir/libexec/multi2hat3s' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pair2hat3s' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pair2hat3s' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/tbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/tbfast' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-homologs.1' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-homologs.1' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafftash_premafft.pl' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafftash_premafft.pl' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mccaskillwrap' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mccaskillwrap' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/f2cl' => '/usr/local/bin/pasta/bin/mafftdir/libexec/f2cl' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/countlen' => '/usr/local/bin/pasta/bin/mafftdir/libexec/countlen' Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/disttbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/disttbfast' Traceback (most recent call last): File "setup.py", line 199, in for files in os.listdir(searchDir): FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/sate-tools-linux/databases'

I checked the sate-tools-linux https://github.com/smirarab/sate-tools-linux repository, and there's no databases folder, which is why this error is getting triggered. Looking at the commit history https://github.com/smirarab/sate-tools-linux/commits/master, it seems like the files in the databases folder were deleted 11 days ago. I'm not sure what these databases were used for nor how their deletion affects PASTA setup, so I won't remove these symlink lines, but someone should look into this

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-- Siavash Mirarab

smirarab commented 6 years ago

I believe this is the results of the recent changes. Can you fix?

On Sun, Apr 15, 2018 at 11:58 AM, Niema Moshiri notifications@github.com wrote:

In the README, in step 5 (run sudo python setup.py develop), I think the setup.py script is expecting Python 3, because I get the following error message:

Traceback (most recent call last): File "setup.py", line 14, in ez_setup.use_setuptools() File "/root/pasta/ez_setup.py", line 98, in use_setuptools return do_download() File "/root/pasta/ez_setup.py", line 92, in do_download egg = download_setuptools(version, download_base, to_dir, download_delay) File "/root/pasta/ez_setup.py", line 127, in download_setuptools import urllib.request, urllib.error, urllib.parse, shutil ImportError: No module named request

In Python 2, it's urllib2.request, not urllib.request, which is why I think it's expecting Python 3. I think this holds true for the other urllib things being imported too (https://docs.python.org/2/ library/urllib.html). It might be good to add a version check or perhaps a try-except block, e.g.:

try: # Python 3 import urllib.request, urllib.error, urllib.parse, shutilexcept: # Python 2

do whatever the correct thing is in Python 2

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-- Siavash Mirarab

zhangwenting0816 commented 6 years ago

after i type 'sudo python setup.py develop' i got notes like these：

Creating link: '/home/bin/pasta-code/pasta/resources/scripts/hmmeralign' => '/home/bin/pasta-code/pasta/bin/hmmeralign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/raxml' => '/home/bin/pasta-code/pasta/bin/raxml' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafft' => '/home/bin/pasta-code/pasta/bin/mafft' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/hmmbuild' => '/home/bin/pasta-code/pasta/bin/hmmbuild' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/hmmalign' => '/home/bin/pasta-code/pasta/bin/hmmalign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign.topology' => '/home/bin/pasta-code/pasta/bin/contralign.topology' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign.params' => '/home/bin/pasta-code/pasta/bin/contralign.params' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/probcons' => '/home/bin/pasta-code/pasta/bin/probcons' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/opal.jar' => '/home/bin/pasta-code/pasta/bin/opal.jar' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fasttreeMP' => '/home/bin/pasta-code/pasta/bin/fasttreeMP' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/raxmlp' => '/home/bin/pasta-code/pasta/bin/raxmlp' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/homologs' => '/home/bin/pasta-code/pasta/bin/homologs' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/clustalw2' => '/home/bin/pasta-code/pasta/bin/clustalw2' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/.gitignore' => '/home/bin/pasta-code/pasta/bin/.gitignore' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fasttree' => '/home/bin/pasta-code/pasta/bin/fasttree' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fakealigner' => '/home/bin/pasta-code/pasta/bin/fakealigner' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/faketree' => '/home/bin/pasta-code/pasta/bin/faketree' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign' => '/home/bin/pasta-code/pasta/bin/contralign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/padaligner' => '/home/bin/pasta-code/pasta/bin/padaligner' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/muscle' => '/home/bin/pasta-code/pasta/bin/muscle' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/prank' => '/home/bin/pasta-code/pasta/bin/prank' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/randtree' => '/home/bin/pasta-code/pasta/bin/randtree' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/bin/mafft' => '/home/bin/pasta-code/pasta/bin/mafftdir/bin/mafft' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndpre' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndpre' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/getlag' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/getlag' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pairlocalalign' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/makedirectionlist' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/makedirectionlist' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mccaskillwrap' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mccaskillwrap' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/setdirection' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/setdirection' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndblast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndblast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/contrafoldwrap' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/contrafoldwrap' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/splittbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/splittbfast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pair2hat3s' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pair2hat3s' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/f2cl' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/f2cl' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/restoreu' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/restoreu' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/regtable2seq' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/regtable2seq' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/tbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/tbfast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-distance' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-distance' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pairash' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pairash' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/countlen' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/countlen' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-homologs.1' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-homologs.1' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/addsingle' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/addsingle' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/multi2hat3s' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/multi2hat3s' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/replaceu' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/replaceu' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/seq2regtable' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/seq2regtable' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/score' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/score' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/sextet5' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/sextet5' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dvtditr' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dvtditr' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft.1' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft.1' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/disttbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/disttbfast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-profile' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-profile' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/setcore' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/setcore' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafftash_premafft.pl' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafftash_premafft.pl' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/rnatest' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/rnatest' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndfast7' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndfast7' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndpre2' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndpre2' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/version' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/version' Path already exists and is linked correctly. /usr/local/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'app' warnings.warn(msg) running develop running egg_info writing PASTA.egg-info/PKG-INFO writing dependency_links to PASTA.egg-info/dependency_links.txt writing requirements to PASTA.egg-info/requires.txt writing top-level names to PASTA.egg-info/top_level.txt reading manifest file 'PASTA.egg-info/SOURCES.txt' writing manifest file 'PASTA.egg-info/SOURCES.txt' running build_ext Creating /usr/local/lib/python3.6/site-packages/PASTA.egg-link (link to .) PASTA 1.8.2 is already the active version in easy-install.pth Installing run_pasta.py script to /usr/local/bin Installing run_pasta_gui.py script to /usr/local/bin Installing run_seqtools.py script to /usr/local/bin

Installed /home/bin/pasta-code/pasta Processing dependencies for PASTA==1.8.2 Searching for dendropy>=4.00 Reading https://pypi.python.org/simple/dendropy/ Downloading https://files.pythonhosted.org/packages/f5/21/17e4fbb1c2a68421eec43930b1e118660c7483229f1b28ba4402e8856884/DendroPy-4.4.0.tar.gz#sha256=f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c

than stop here no continuing could you help me ?

smirarab commented 6 years ago

Hmm. Not sure. Dwndropy is big, so perhaps it just takes time?

On Tue, Sep 25, 2018 at 7:35 AM zhangwenting0816 notifications@github.com wrote:

after i type 'sudo python setup.py develop' i got notes like these：

Creating link: '/home/bin/pasta-code/pasta/resources/scripts/hmmeralign' => '/home/bin/pasta-code/pasta/bin/hmmeralign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/raxml' => '/home/bin/pasta-code/pasta/bin/raxml' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafft' => '/home/bin/pasta-code/pasta/bin/mafft' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/hmmbuild' => '/home/bin/pasta-code/pasta/bin/hmmbuild' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/hmmalign' => '/home/bin/pasta-code/pasta/bin/hmmalign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign.topology' => '/home/bin/pasta-code/pasta/bin/contralign.topology' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign.params' => '/home/bin/pasta-code/pasta/bin/contralign.params' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/probcons' => '/home/bin/pasta-code/pasta/bin/probcons' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/opal.jar' => '/home/bin/pasta-code/pasta/bin/opal.jar' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fasttreeMP' => '/home/bin/pasta-code/pasta/bin/fasttreeMP' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/raxmlp' => '/home/bin/pasta-code/pasta/bin/raxmlp' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/homologs' => '/home/bin/pasta-code/pasta/bin/homologs' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/clustalw2' => '/home/bin/pasta-code/pasta/bin/clustalw2' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/.gitignore' => '/home/bin/pasta-code/pasta/bin/.gitignore' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fasttree' => '/home/bin/pasta-code/pasta/bin/fasttree' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fakealigner' => '/home/bin/pasta-code/pasta/bin/fakealigner' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/faketree' => '/home/bin/pasta-code/pasta/bin/faketree' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign' => '/home/bin/pasta-code/pasta/bin/contralign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/padaligner' => '/home/bin/pasta-code/pasta/bin/padaligner' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/muscle' => '/home/bin/pasta-code/pasta/bin/muscle' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/prank' => '/home/bin/pasta-code/pasta/bin/prank' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/randtree' => '/home/bin/pasta-code/pasta/bin/randtree' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/bin/mafft' => '/home/bin/pasta-code/pasta/bin/mafftdir/bin/mafft' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndpre' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndpre' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/getlag' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/getlag' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pairlocalalign' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/makedirectionlist' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/makedirectionlist' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mccaskillwrap' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mccaskillwrap' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/setdirection' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/setdirection' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndblast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndblast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/contrafoldwrap' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/contrafoldwrap' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/splittbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/splittbfast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pair2hat3s' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pair2hat3s' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/f2cl' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/f2cl' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/restoreu' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/restoreu' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/regtable2seq' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/regtable2seq' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/tbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/tbfast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-distance' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-distance' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pairash' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pairash' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/countlen' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/countlen' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-homologs.1' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-homologs.1' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/addsingle' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/addsingle' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/multi2hat3s' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/multi2hat3s' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/replaceu' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/replaceu' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/seq2regtable' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/seq2regtable' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/score' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/score' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/sextet5' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/sextet5' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dvtditr' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dvtditr' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft.1' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft.1' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/disttbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/disttbfast' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-profile' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-profile' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/setcore' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/setcore' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/ mafftash_premafft.pl' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/ mafftash_premafft.pl' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/rnatest' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/rnatest' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndfast7' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndfast7' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndpre2' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndpre2' Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/version' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/version' Path already exists and is linked correctly. /usr/local/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'app' warnings.warn(msg) running develop running egg_info writing PASTA.egg-info/PKG-INFO writing dependency_links to PASTA.egg-info/dependency_links.txt writing requirements to PASTA.egg-info/requires.txt writing top-level names to PASTA.egg-info/top_level.txt reading manifest file 'PASTA.egg-info/SOURCES.txt' writing manifest file 'PASTA.egg-info/SOURCES.txt' running build_ext Creating /usr/local/lib/python3.6/site-packages/PASTA.egg-link (link to .) PASTA 1.8.2 is already the active version in easy-install.pth Installing run_pasta.py script to /usr/local/bin Installing run_pasta_gui.py script to /usr/local/bin Installing run_seqtools.py script to /usr/local/bin

Installed /home/bin/pasta-code/pasta Processing dependencies for PASTA==1.8.2 Searching for dendropy>=4.00 Reading https://pypi.python.org/simple/dendropy/ Downloading https://files.pythonhosted.org/packages/f5/21/17e4fbb1c2a68421eec43930b1e118660c7483229f1b28ba4402e8856884/DendroPy-4.4.0.tar.gz#sha256=f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c

than stop here no continuing could you help me ?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/smirarab/pasta/issues/30#issuecomment-424368251, or mute the thread https://github.com/notifications/unsubscribe-auth/AAybuAqYTXNZT3Av0dbc33C-UQ8a4tCVks5uej8ygaJpZM4TVmU6 .

-- Siavash Mirarab

smirarab commented 5 years ago

Niema, was this fixed?

niemasd commented 5 years ago

I think the DendroPy issue mentioned by zhangwenting0816 is not the same as the issue I had encountered. I believe I fixed my issue in my Docker image by having the Dockerfile use the old commit of the "sate-tools-linux" repository. I don't remember if the master branch of "sate-tools-linux" was ever fixed accordingly or if we ever fixed the master branch of PASTA itself