lucruzz/parslrna-seq repository overview

ParslRNA-Seq is a workflow for RNA sequencing that uses the Parallel Scripting Library - Parsl for parallel processing (see on GitHub⁠).

The container includes:

• Parsl, version 1.0
• Python, version 3.8.2
• Bowtie, version 2.3
• Samtools, version 1.10
• Picard, version 2.18
• HTSeq, version 0.13.5
• R, version 3.5.2

To run it, create a directory on the host machine with the following hierarchy of directories and mount them in the container:

1. inputs
   • input files
2. outputs
3. table.csv
4. gtf
   • <<file>>.gtf
5. genomic_base
   • genomic-base-files

To run ParslRNA-Seq in the container, run the following command and keep monitoring the outputs directory:

$ sudo docker run -d -v diretorio_maquina_hospedeira:/workdir -e
$ RNASEQ_TABLE_CSV=/workdir/table.csv -e
$ RNASEQ_GENETIC_BASE=/workdir/base_genetica/prefixo_arquivo -e
$ RNASEQ_NUM_THREADS=4 -e RNASEQ_INPUTS=/workdir/inputs/ -e
$ RNASEQ_OUTPUTS=/workdir/outputs/ -e RNASEQ_GTF=/workdir/arquivo.gtf
$ rnaseq:1.0 /RNA-seq/rna-seq.sh`