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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 installrunning installrunning bdist_eggrunning egg_infowriting pangolin.egg-info/PKG-INFOwriting dependency_links to pangolin.egg-info/dependency_links.txtwriting entry points to pangolin.egg-info/entry_points.txtwriting requirements to pangolin.egg-info/requires.txtwriting top-level names to pangolin.egg-info/top_level.txtreading 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/eggrunning install_librunning build_pycreating build/bdist.macosx-10.9-x86_64/eggcreating build/bdist.macosx-10.9-x86_64/egg/pangolincopying build/lib/pangolin/command.py -> build/bdist.macosx-10.9-x86_64/egg/pangolincopying build/lib/pangolin/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/pangolincreating build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/type_variants.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/report_classes.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/pangofunks.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/custom_logger.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/pangolearn.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/utils.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/report_results.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/pangolearn.smk -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscopying build/lib/pangolin/scripts/log_handler_handle.py -> build/bdist.macosx-10.9-x86_64/egg/pangolin/scriptscreating build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/config_p.3.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/config_p.2.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/config_p.1.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/config_b.1.1.7.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/config_b.1.351.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/reference.fasta -> build/bdist.macosx-10.9-x86_64/egg/pangolin/datacopying build/lib/pangolin/data/config_b.1.214.2.csv -> build/bdist.macosx-10.9-x86_64/egg/pangolin/databyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/command.py to command.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/__init__.py to __init__.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/type_variants.py to type_variants.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/report_classes.py to report_classes.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/pangofunks.py to pangofunks.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/__init__.py to __init__.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/custom_logger.py to custom_logger.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/pangolearn.py to pangolearn.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/utils.py to utils.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/report_results.py to report_results.cpython-37.pycbyte-compiling build/bdist.macosx-10.9-x86_64/egg/pangolin/scripts/log_handler_handle.py to log_handler_handle.cpython-37.pyccreating build/bdist.macosx-10.9-x86_64/egg/EGG-INFOinstalling scripts to build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptsrunning install_scriptsrunning build_scriptscreating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/type_variants.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/report_classes.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/pangofunks.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/custom_logger.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/pangolearn.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/utils.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/report_results.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/pangolearn.smk -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptscopying build/scripts-3.7/log_handler_handle.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scriptschanging mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/type_variants.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/report_classes.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/pangofunks.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/custom_logger.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/pangolearn.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/utils.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/report_results.py to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/pangolearn.smk to 755changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/log_handler_handle.py to 755copying pangolin.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcopying pangolin.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcopying pangolin.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcopying pangolin.egg-info/entry_points.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcopying pangolin.egg-info/not-zip-safe -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcopying pangolin.egg-info/requires.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcopying pangolin.egg-info/top_level.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFOcreating 'dist/pangolin-2.4.2-py3.7.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to itremoving 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)Processing pangolin-2.4.2-py3.7.eggremoving '/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.eggExtracting pangolin-2.4.2-py3.7.egg to /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packagespangolin 2.4.2 is already the active version in easy-install.pthInstalling type_variants.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling report_classes.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling pangofunks.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling custom_logger.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling pangolearn.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling utils.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling report_results.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling pangolearn.smk script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling log_handler_handle.py script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalling pangolin script to /usr/local/Caskroom/miniconda/base/envs/pangolin/binInstalled /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packages/pangolin-2.4.2-py3.7.eggProcessing dependencies for pangolin==2.4.2...Using /usr/local/Caskroom/miniconda/base/envs/pangolin/lib/python3.7/site-packagesFinished processing dependencies for pangolin==2.4.2(pangolin) art@Wernstrom pangolin % pangolinusage: pangolin <query> [options]pangolin: Phylogenetic Assignment of Named Global Outbreak LINeagespositional 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.
The text was updated successfully, but these errors were encountered:
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.
Note
--xz
option is missing.The text was updated successfully, but these errors were encountered: