CLEANUP: Use same SAMTOOLS everywhere

UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline

https://github.com/UCSF-Costello-Lab/LG3_Pipeline

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CLEANUP: Use same SAMTOOLS everywhere #139

Closed HenrikBengtsson closed 2 years ago

HenrikBengtsson commented 4 years ago

$ grep -E "^SAMTOOLS=" -r --include="*.sh"
scripts/Merge_QC.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/Recal_step.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/FixReadGroups.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/Recal.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/Recal_pass2.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/Align_mem.sh:SAMTOOLS=samtools
scripts/Merge.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/Align_fastq.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools

HenrikBengtsson commented 2 years ago

Meeting notes from 2021-10-01:

scripts/Align_mem.sh:SAMTOOLS=samtools

This is not used in the default pipeline, because we still use the old BWA aligner. Thus, if we change, our redundancy checks won't test it anyway.

Decision:

[x] Update to SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools to make sure we're all running the same version and to align with the rest of the code.
[x] Document this change in the NEWS file.

Hopefully it won't make a difference; we just have to cross our fingers that it wont

HenrikBengtsson commented 2 years ago

Turns out that this was fixed in the 2020-05-26 release, cf. https://github.com/UCSF-Costello-Lab/LG3_Pipeline/blob/develop/NEWS.md#software-quality. Though, that version was never formally "released". The version that's on TIPCC is 2020-05-16.