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Work in progress...

Within $PWD, we have:

./tmp: a working directory
./data: test data for each tool; in turn, we have a sub-folder for each tool to test

Here are commands to execute to run a test of:

Simka:

docker run --rm -i -t -v $PWD/tmp/:/tmp -v $PWD/data/simka/:/simka gatb_tools_machine -c simka -- -in /simka/simka_input.txt -out /tmp/simka_results/ -out-tmp /tmp/simka_temp_output

Simka visualization:

docker run --rm -i -t -v $PWD/tmp/:/tmp gatb_tools_machine -c simka-visu -- -in /tmp/simka_results/ -out /tmp/simka_results/ -pca -heatmap -tree

Bloocoo:

docker run --rm -i -t -v $PWD/tmp/:/tmp -v $PWD/data/bloocoo/:/bloocoo gatb_tools_machine -c bloocoo -- -file /bloocoo/errclose.fasta -out /tmp/errclose_bloocoo_corr_errs.tab -kmer-size 31 -abundance-min 5 -err-tab