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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

MetaBloocoo:

cd $PWD/data/bloocoo
curl -O http://downloads.hmpdacc.org/data/Illumina/anterior_nares/SRS018585.tar.bz2
tar -xjf SRS018585.tar.bz2
cd ../..
docker run --rm -i -t -v $PWD/tmp/:/tmp -v /Users/pdurand/tmp/nosave/gatb-tools-machine/data/bloocoo/:/bloocoo gatb_tools_machine -c metabloocoo -- count -file /bloocoo/SRS018585/SRS018585.denovo_duplicates_marked.trimmed.1.fastq -out /tmp/SRS018585

DSK:

docker run --rm -i -t -v $PWD/tmp/:/tmp -v $PWD/data/dsk/:/dsk gatb_tools_machine -c dsk -- -file /dsk/read50x_ref10K_e001.fasta.gz -kmer-size 27 -out /tmp/dsk27 -max-memory 200 -verbose 0
docker run --rm -i -t -v $PWD/tmp/:/tmp gatb_tools_machine -c h5dump -- -y -d histogram/histogram /tmp/dsk27.h5 | grep "^\ *[0-9]" | tr -d " " | tr -d "," | paste - - > $PWD/tmp/dsk27.histo

MindTheGap:

docker run --rm -i -t -v $PWD/tmp/:/tmp -v $PWD/data/MindTheGap/:/mdg gatb_tools_machine -c MindTheGap -- find -in /mdg/master.fasta -ref /mdg/deleted.fasta -kmer-size 31 -out /tmp/mdg_find -insert-only

Short Read Connector:

docker run --rm -i -t -v $PWD/tmp/:/tmp -v $PWD/data/ShortReadConnector/:/src gatb_tools_machine -c rconnector -- -b /src/c1.fasta.gz -q /src/fof.txt -p src_linker

DiscoSNP++:

docker run --rm -i -t -v $PWD/tmp/:/tmp -v $PWD/data/DiscoSnp/:/disco gatb_tools_machine -c discosnp -- -r /disco/fof.txt -T