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ArtPoon / pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.
GNU General Public License v3.0
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Problems with local install on macOS #5

Open ArtPoon opened 3 years ago

ArtPoon commented 3 years ago

I think my package managers are all fouled up on my home Mac. I can install and run my modified code on my remote workstation running Ubuntu, but the executable is not being updated on my Mac.

(pangolin) art@Wernstrom pangolin % grep -r xz . | head -n3
./pangolin/command.py:    compression.add_argument("--xz", action="store_true", help="Query files are xz-compressed.")
./pangolin/command.py:    if args.xz:
Binary file ./docs/logo.png matches
(pangolin) art@Wernstrom pangolin % python setup.py install
running install
running bdist_egg
running egg_info
writing pangolin.egg-info/PKG-INFO
writing dependency_links to pangolin.egg-info/dependency_links.txt
writing entry points to pangolin.egg-info/entry_points.txt
writing requirements to pangolin.egg-info/requires.txt
writing top-level names to pangolin.egg-info/top_level.txt
reading manifest file 'pangolin.egg-info/SOURCES.txt'
writing manifest file 'pangolin.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-10.9-x86_64/egg
creating build/bdist.macosx-10.9-x86_64/egg/pangolin
copying build/lib/pangolin/command.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin
copying build/lib/pangolin/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin
creating build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/type_variants.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/report_classes.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/pangofunks.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/custom_logger.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/pangolearn.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/utils.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/report_results.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/pangolearn.smk -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
copying build/lib/pangolin/scripts/log_handler_handle.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts
creating build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/config_p.3.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/config_p.2.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/config_p.1.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/config_b.1.1.7.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/config_b.1.351.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/reference.fasta -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
copying build/lib/pangolin/data/config_b.1.214.2.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/data
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/command.py to command.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/type_variants.py to type_variants.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/report_classes.py to report_classes.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/pangofunks.py to pangofunks.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/custom_logger.py to custom_logger.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/pangolearn.py to pangolearn.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/report_results.py to report_results.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/log_handler_handle.py to log_handler_handle.cpython-37.pyc
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
installing scripts to build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/type_variants.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/report_classes.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/pangofunks.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/custom_logger.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/pangolearn.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/utils.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/report_results.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/pangolearn.smk -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/log_handler_handle.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/type_variants.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/report_classes.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/pangofunks.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/custom_logger.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/pangolearn.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/utils.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/report_results.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/pangolearn.smk to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/log_handler_handle.py to 755
copying pangolin.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying pangolin.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying pangolin.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying pangolin.egg-info/entry_points.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying pangolin.egg-info/not-zip-safe -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying pangolin.egg-info/requires.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying pangolin.egg-info/top_level.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
creating 'dist/pangolin-2.4.2-py3.7.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it
removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)
Processing pangolin-2.4.2-py3.7.egg
removing '/usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packages/pangolin-2.4.2-py3.7.egg' (and everything under it)
creating /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packages/pangolin-2.4.2-py3.7.egg
Extracting pangolin-2.4.2-py3.7.egg to /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packages
pangolin 2.4.2 is already the active version in easy-install.pth
Installing type_variants.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing report_classes.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing pangofunks.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing custom_logger.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing pangolearn.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing utils.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing report_results.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing pangolearn.smk script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing log_handler_handle.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin
Installing pangolin script to /usr/local/Caskroom/miniconda/base/envs/pangolin/bin

Installed /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packages/pangolin-2.4.2-py3.7.egg
Processing dependencies for pangolin==2.4.2

...

Using /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packages
Finished processing dependencies for pangolin==2.4.2
(pangolin) art@Wernstrom pangolin % pangolin
usage: pangolin <query> [options]

pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages

positional arguments:
  query                 Query fasta file of sequences to analyse.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTDIR, --outdir OUTDIR
                        Output directory. Default: current working directory
  --outfile OUTFILE     Optional output file name. Default: lineage_report.csv
  --alignment           Optional alignment output.
  -d DATADIR, --datadir DATADIR
                        Data directory minimally containing a fasta alignment
                        and guide tree
  --tempdir TEMPDIR     Specify where you want the temp stuff to go. Default:
                        $TMPDIR
  --no-temp             Output all intermediate files, for dev purposes.
  --decompress-model    Permanently decompress the model file to save time
                        running pangolin.
  --max-ambig MAXAMBIG  Maximum proportion of Ns allowed for pangolin to
                        attempt assignment. Default: 0.5
  --min-length MINLEN   Minimum query length allowed for pangolin to attempt
                        assignment. Default: 25000
  --panGUIlin           Run web-app version of pangolin
  --verbose             Print lots of stuff to screen
  -t THREADS, --threads THREADS
                        Number of threads
  -v, --version         show program's version number and exit
  -pv, --pangoLEARN-version
                        show pangoLEARN's version number and exit
  --update              Automatically updates to latest release of pangolin
                        and pangoLEARN, then exits
  --gzip                Query files are gzip-compressed.
(pangolin) art@Wernstrom pangolin %

Note --xz option is missing.

ArtPoon commented 3 years ago

Had to nuke the entire folder, re-clone repo and reinstall