search

suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
Other
226 stars 50 forks source link

Utility scripts in Docker container #170

Closed mattdoug604 closed 1 year ago

mattdoug604 commented 1 year ago

Hi, are the utility scripts included in the Docker container? If not, is it possible to add them in?

I'm specifically interested in including the extract_fusion-supporting_alignments.sh script in a workflow, but right now that does not seem possible if I want to use the container.

Example using Singularity:

$ singularity exec uhrigs-arriba-2.2.1.img extract_fusion-supporting_alignments.sh
/.singularity.d/actions/exec: 21: exec: extract_fusion-supporting_alignments.sh: not found

Thanks for you help.

mattdoug604 commented 1 year ago

Oh nevermind, I see it is in there:

$ singularity exec uhrigs-arriba-2.2.1.img /arriba_v2.2.1/scripts/extract_fusion-supporting_alignments.sh
Usage: extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam output_prefix

Description: This script takes fusion predictions from Arriba (fusions.tsv) and extracts the fusion-supporting alignments listed in the column 'read_identifiers' from the given input BAM file (Aligned.sortedByCoord.out.bam). The input BAM file must be sorted and indexed. For each fusion, a separate BAM file is created containing only the fusion-supporting alignments. The created BAM files are named after the given output prefix and the rank of the fusion in Arriba's output file.