[FAILED_ANALYSIS]: Problems with manta in varcall_py27 container

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

https://balsamic.readthedocs.io/

MIT License

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[FAILED_ANALYSIS]: Problems with manta in varcall_py27 container #967

Closed ashwini06 closed 2 years ago

ashwini06 commented 2 years ago

The current varcall_py27 develop container has issues while running manta. Missing the script

bash: line 7: /opt/conda/share/manta-1.6.0-1/libexec/convertInversion.py: No such file or directory

Full detailed log is here: /home/proj/stage/cancer/cases/unitedbeagle/logs/BALSAMIC.unitedbeagle.manta_tumor_normal.83.sh_3185132.err

New test container builts are located here: /home/proj/long-term-stage/cancer/UMI_analysis_runs_APJ/balsamic_cache/9.0.1/containers

ashwini06 commented 2 years ago

Seems like now the new path for this script convertInversion.py is located in /opt/conda/share/manta-1.6.0-2/libexec/ instead of /opt/conda/share/manta-1.6.0-1/

Solution: Change the related lines in the manta rules:

for eg: https://github.com/Clinical-Genomics/BALSAMIC/blob/2e7ef3d5d437424b0dc9b75253152fbc90a92fbf/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule#L25

khurrammaqbool commented 2 years ago

fixed in https://github.com/Clinical-Genomics/BALSAMIC/pull/966