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transipedia/dekupl-run

By transipedia

•Updated about 5 years ago

DE-kupl is a pipeline that finds differentially expressed k-mers between RNA-Seq datasets.

Image
0

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transipedia/dekupl-run repository overview

⁠Run dekupl-run with docker
⁠Pull
docker pull transipedia/dekupl-run
⁠Run

You may need to mount some volumes :

  • Your my-config.json to /dekupl/my-config.json
  • Your fastq_dir (the one defined in your config.json) to /dekupl/FASTQ_DIR
  • Your output_dir (the one defined in your config.json) to /dekupl/OUTPUT_DIR
  • Any other necessary folder depending on your config.json
⁠Example
docker run --rm -v ${PWD}my-config.json:/dekupl/my-config.json -v ${PWD}/data:/dekupl/data  -v ${PWD}/results:/dekupl/results transipedia/dekupl-run --configfile my-config.json  -jNB_THREADS --resources ram=MAX_MEMORY -p
⁠Run dekupl-run with singularity
singularity pull docker://transipedia/dekupl-run
./dekupl-run.simg --configfile my-config.json -jNB_THREADS --resources ram=MAX_MEMORY -p

OR

singularity build dekupl-run.img docker://transipedia/dekupl-run
singularity run ./dekupl-run.img --configfile my-config.json -jNB_THREADS --resources ram=MAX_MEMORY -p

You don't need to mount any volumes with singularity, but you must have your config.json and your inputs file in the directory where you are running dekupl-run.

Tag summary

Content type

Image

Digest

Size

767.8 MB

Last updated

about 5 years ago

docker pull transipedia/dekupl-run