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gea.def
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gea.def
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Bootstrap: localimage
From: /home/aaron/containers/locallibrary/geacontV001
#The PATH to the local image is user specific.
%files
#files are required for recreating the container. The PATH to the files (e.g. /home/aaron/singfiles/shovill/trimmomatic) is user specific
#databases.tar.gz is the copy of the databases used in the paper and can be provided on request.
/home/aaron/singfiles/GEAbash /usr/local/src
/home/aaron/singfiles/databases.tar.gz /usr/local/src
%help
geacont version 0.0.1 was built on October 23, 2023 on the ubuntu jammy (22.0.4) operating system using the command sudo apptainer build geacont gea.def on apptainer version
1.2.4. see gea_baseimage.def on github. geacont version 0.0.3 was built on May 14, 2024 on geacont version 0.0.1 (apptainer version 1.3.1).
Changelog: GEAbash version 0.0.3 fixes 1. a bug that caused the pipeline to procced to assembly despite invalid user designated taxon.
2. a bug that caused undesired awk floating point calculations for some non-USA users.
This version also removes the largest intermediate files to significantly reduce the size of the output results folder.
Software Versions in container: SPAdes (version 3.15), blast (version 2.12), skesa (version 2.4), shovill (version 1.1), fimtyper (version 1.1), resfinder (version 4.3),
mlst (version 2023-02-06), virulencefinder (version 2020-02-06), serotypefinder (version 2018-09-24), plasmidfinder (2020-02-07), ezclermont (version 0.7),
stats.sh (version March 3, 2020) and SeqSero2 (version 1.1).
The software in this container Runs the end-to-end Gammaproteobacteria Epidemiologic Annotation pipeline.
Before running the pipeline, this container must be placed in $HOME/software using the command: `cp geacont $HOME/software/` without backticks
After placing this container in $HOME/software, extract the bash script from the container with
`apptainer exec $HOME/software/geacont cp /usr/local/src/GEAbash $HOME/software/`
Then you can get the full pipleline help message with `$HOME/software/GEAbash`
To get this help message: `apptainer run-help geacont`
To get help with constituent programs used in the pipeline (not exhaustive):
`apptainer exec geacont fimtyper.pl -h`
`apptainer exec geacont shovill -h`
`apptainer exec geacont blastn -h`
`apptainer exec geacont skesa -h`
`apptainer exec --app cge geacont mlst.py -h`
`apptainer exec --app cge geacont virulencefinder.py -h`
`apptainer exec --app cge geacont serotypefinder.py -h`
`apptainer exec --app cge geacont plasmidfinder.py -h`
`apptainer exec --app resfinder geacont python3 -m resfinder -h`
`apptainer exec --app clermont geacont ezclermont -h`
`apptainer exec --app seqsero geacont SeqSero2_package.py -h`