lts_workflows_sm_scrnaseq documentation

Documentation Status

single-cell RNA sequencing snakemake workflow

  • Free software: GNU General Public License v3

Quickstart

$ conda create -n py2.7 python=2.7 rpkmforgenes=1.0.1 rseqc=2.6.4
$ conda create -n lts-workflows-sm-scrnaseq python=3.6
$ source activate lts-workflows-sm-scrnaseq
$ conda install -c scilifelab-lts lts-workflows-sm-scrnaseq
$ lts_workflows_sm_scrnaseq
$ lts_workflows_sm_scrnaseq -l
$ lts_workflows_sm_scrnaseq all -d /path/to/workdir --configfile config.yaml
$ lts_workflows_sm_scrnaseq --use-conda all -d /path/to/workdir --configfile config.yaml
$ docker pull scilifelablts/lts-workflows-sm-scrnaseq
$ docker run scilifelablts/lts-workflows-sm-scrnaseq
$ docker run -v /path/to/workdir:/workspace -w /workspace scilifelablts/lts-workflows-sm-scrnaseq -l
$ docker run -v /path/to/workdir:/workspace -w /workspace scilifelablts/lts-workflows-sm-scrnaseq all

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