Comments (16)
jayramr
commented on July 24, 2024
Any update on this?
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jayramr
commented on July 24, 2024
Dear @simonrasmu
I would request you to release the versioning for this package as per
https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository#creating-a-release
Please advise
Thanks
Jay
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simonrasmu
commented on July 24, 2024
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joacjo
commented on July 24, 2024
Dear @jayramr - Kudos to your efforts on making Phamb available on Bioconda!
Apologize for our delayed response to this issue.
A versioned release is now available. Thank you!
Let us know if there are anything we can do.
Best,
Joachim
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jayramr
commented on July 24, 2024
Thank you so much
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jayramr
commented on July 24, 2024
Dear @joacjo
I'm facing some issue with building this package in bioconda.
As per the community recommendation, could you convert the same into a python package?
So i can easily push/merge this as a bioconda package
Please advise
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joacjo
commented on July 24, 2024
Hi Jay
I created a python package on the dev branch, can you check if that solves your issue with creating the bioconda package? Also let me know if you face any issues with the installation.
It would be great to know if this solves the issue before I push it to master.
Best,
Joachim
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jayramr
commented on July 24, 2024
Sure thanks, let me try to test this today and update you
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jayramr
commented on July 24, 2024
@joacjo i tried to test this dev version.
Here is my testing flow
-> Create a conda env with python 3.9
-> python setup.py install ( no errors found )
(phamb) jr5241@DCLAP-V1342-CGSB:/data/install/jaya/phamb$ python setup.py install
running install
/data/miniconda3/envs/phamb/lib/python3.7/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
setuptools.SetuptoolsDeprecationWarning,
/data/miniconda3/envs/phamb/lib/python3.7/site-packages/setuptools/command/easy_install.py:147: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
EasyInstallDeprecationWarning,
running bdist_egg
running egg_info
creating phamb.egg-info
writing phamb.egg-info/PKG-INFO
writing dependency_links to phamb.egg-info/dependency_links.txt
writing top-level names to phamb.egg-info/top_level.txt
writing manifest file 'phamb.egg-info/SOURCES.txt'
reading manifest file 'phamb.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'phamb.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/phamb
copying phamb/vambtools.py -> build/lib/phamb
copying phamb/split_contigs.py -> build/lib/phamb
copying phamb/run_RF_modules.py -> build/lib/phamb
copying phamb/run_RF.py -> build/lib/phamb
copying phamb/__init__.py -> build/lib/phamb
creating build/lib/phamb/dbs
copying phamb/dbs/RF_model.python39.sav -> build/lib/phamb/dbs
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/phamb
creating build/bdist.linux-x86_64/egg/phamb/dbs
copying build/lib/phamb/dbs/RF_model.python39.sav -> build/bdist.linux-x86_64/egg/phamb/dbs
copying build/lib/phamb/vambtools.py -> build/bdist.linux-x86_64/egg/phamb
copying build/lib/phamb/split_contigs.py -> build/bdist.linux-x86_64/egg/phamb
copying build/lib/phamb/run_RF_modules.py -> build/bdist.linux-x86_64/egg/phamb
copying build/lib/phamb/run_RF.py -> build/bdist.linux-x86_64/egg/phamb
copying build/lib/phamb/__init__.py -> build/bdist.linux-x86_64/egg/phamb
byte-compiling build/bdist.linux-x86_64/egg/phamb/vambtools.py to vambtools.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/phamb/split_contigs.py to split_contigs.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/phamb/run_RF_modules.py to run_RF_modules.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/phamb/run_RF.py to run_RF.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/phamb/__init__.py to __init__.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.7
copying and adjusting phamb/run_RF.py -> build/scripts-3.7
copying and adjusting phamb/split_contigs.py -> build/scripts-3.7
copying phamb/vambtools.py -> build/scripts-3.7
copying and adjusting phamb/run_RF_modules.py -> build/scripts-3.7
changing mode of build/scripts-3.7/run_RF.py from 664 to 775
changing mode of build/scripts-3.7/split_contigs.py from 664 to 775
changing mode of build/scripts-3.7/run_RF_modules.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/vambtools.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/split_contigs.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/run_RF_modules.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/run_RF.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/vambtools.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/split_contigs.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/run_RF_modules.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/run_RF.py to 775
copying phamb.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying phamb.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying phamb.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying phamb.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
phamb.__pycache__.run_RF.cpython-37: module references __file__
creating dist
creating 'dist/phamb-1.0.1-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing phamb-1.0.1-py3.7.egg
creating /data/miniconda3/envs/phamb/lib/python3.7/site-packages/phamb-1.0.1-py3.7.egg
Extracting phamb-1.0.1-py3.7.egg to /data/miniconda3/envs/phamb/lib/python3.7/site-packages
Adding phamb 1.0.1 to easy-install.pth file
Installing vambtools.py script to /data/miniconda3/envs/phamb/bin
Installing split_contigs.py script to /data/miniconda3/envs/phamb/bin
Installing run_RF_modules.py script to /data/miniconda3/envs/phamb/bin
Installing run_RF.py script to /data/miniconda3/envs/phamb/bin
Installed /data/miniconda3/envs/phamb/lib/python3.7/site-packages/phamb-1.0.1-py3.7.egg
Processing dependencies for phamb==1.0.1
Finished processing dependencies for phamb==1.0.1
Then I tested the phamb using below command. but i got error as numpy, sklearn missing
-> run_RF.py
I have two questions
- What are prerequsites for installing phamb?
- Once this is installed how to test whether this module/application is working ?
Thanks
Jay
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joacjo
commented on July 24, 2024
Hi Jay
I specified the following the dependency for scikit learn mamba install -c conda-forge -c bioconda scikit-learn=1.0.2
I can try to package the programme with this dependency, such that it is installed automatically by pip.
Best,
Joachim
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jayramr
commented on July 24, 2024
Hi @joacjo yes please pls package them, i will test.
Also please advise for below point
"Once this is installed how to test whether this module/application is working ?"
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joacjo
commented on July 24, 2024
Hi Jay
Check out the updated dev branch. You can test the installation by
pip install -e .
### Test installation
mkdir -p testout
run_RF.py test/contigs.fna.gz test/clusters.tsv test testout
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jayramr
commented on July 24, 2024
Thanks this worked well :) please push this as official version one
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joacjo
commented on July 24, 2024
Great!
Note the new tag: v.1.0.1.
Best,
Joachim
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jayramr
commented on July 24, 2024
Hi @joacjo phamb is integrated to bioconda.
https://anaconda.org/bioconda/phamb
Please close this tracker
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joacjo
commented on July 24, 2024
Great. I will update the README with instructions for now Bioconda based installation.
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Related Issues (20)
- modified header names in PHAMB HOT 4
- Parsing deepvirfinder line 512, in _parse_dvf_row contig_name, length, score, pvalue = line[:-1].split() HOT 2
- contig length HOT 1
- Update shebang lines in phamb python scripts HOT 2
- High number of bacterial genes in phamb assembled bins HOT 3
- split_contigs.py produces empty files HOT 1
- Can PHAMB output comparable performance on environmental metagenome compared to gut metagenome HOT 1
- split_contigs.py produces empty files HOT 2
- how to evaluate the bin-annotations? HOT 1
- What are the criteria of RF model HOT 2
- The predicted 'viral' number in 'vambbins_RF_predictions.txt' is inconsistent with the actual number in 'vamb_bins.1.fna'? HOT 1
- Binning question, how to use vamb? HOT 7
- 'run_RF.py' operation problem HOT 1
- how to get the file 'clusters.tsv' ?
- VAE or AAE? HOT 1
- How to Run - not in parallel - quick and dirty HOT 1
- interpret the results of RF model
- Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing) HOT 2
- category of viruses identified by PHAMB ?
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