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A Command Line Interface (CLI) for Statistical Analysis of Metagenomic Profiles (STAMP)

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stamp-cmd

A Command Line Interface (CLI) for Statistical Analysis of Metagenomic Profiles (STAMP)

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Information regarding STAMP can be found at: http://kiwi.cs.dal.ca/Software/STAMP

Docker Usage

$ docker run -t -v ${PWD}/example:/data --name stamp1 hotdogee/stamp-cmd -i /data/otu.g.spf -g /data/Grouping.txt -d /out
$ docker cp stamp1:/out .
$ docker container rm stamp1

Local Usage

$ python stamp_cmd.py -h
usage: stamp_cmd.py [-h] -i PROFILE -g METADATA [-d OUTPUT] [-p PLOT]
                    [-t TABLE]

optional arguments:
  -h, --help            show this help message and exit
  -i PROFILE, --profile PROFILE
                        Path to the profile file
  -g METADATA, --metadata METADATA
                        Path to the group metadata file
  -d OUTPUT, --output OUTPUT
                        Output directory (default: output)
  -p PLOT, --plot PLOT  
                        Plot filename template (default: {g1}-vs-{g2}.psig.png)
  -t TABLE, --table TABLE
                        Table filename template (default: {g1}-vs-{g2}.test.xls)

Docker build

$ docker build -f ./mkl/Dockerfile -t hotdogee/stamp-cmd:1.5.0 .
$ docker tag hotdogee/stamp-cmd:1.5.0 hotdogee/stamp-cmd:latest
$ docker push hotdogee/stamp-cmd

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A Command Line Interface (CLI) for Statistical Analysis of Metagenomic Profiles (STAMP)

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