CLEANUP: Set PYTHON to stable python version and use everywhere

Semi-randomly, some scripts call python on the PATH;

$ grep -E "^(|.* )python " scripts/*.sh
scripts/annotate_mutations_from_bam.sh:python "${LG3_HOME}/scripts/annotate_mutations_from_bam.py" "${PATIENT}.snvs" "${CONV}" "${PATIENT}" "${PROJECT}" || error "annotate_mutations_from_bam.py failed"
scripts/combine_snvs.sh:python "${LG3_HOME}/scripts/combine_snvs.py" "${PATIENT}" "${PROJECT}" "${CONV}" "${PATIENT}.snvs" || error "combine_snvs.py failed"
scripts/libID_to_patientID.sh:python "${LG3_HOME}/scripts/libID_to_patientID.py" "${MUTFILE}" "${PATIENT}" "${OUTFILE}" "${CONV}" || error "libID_to_patientID.py failed"
scripts/mutation_overlaps.sh:python "${LG3_HOME}/scripts/mutation_overlaps.py" "${MUTFILE}" "${PATIENT}" "${OUTFILE}" || error "mutation_overlaps.py failed"
scripts/Mutect2_TvsN.sh:python --version
scripts/mutect_coverage_intersection_mutations.sh:python "${PYTHON_CONV_PAT_WIG2BED}" "${PATIENT}" "${PROJECT}" "${CONV}"  || error "${PYTHON_CONV_PAT_WIG2BED} failed"
scripts/pindel_filter.sh:python "${PYTHON_PINDEL_FILTER}" "${datafile}"
scripts/pindel_setup.sh:python "${PYTHON_PINDEL_SETUP}" "${patient_ID}" "${proj}" "${patIDs}"
scripts/runLOH_ivan.sh:python "${PYTHON_RUNMAF}" "${PATIENT}" "${PROJECT}" "${CONV}" || error "${PYTHON_RUNMAF} failed"

and some call $PYTHON:

grep -F '$PYTHON ' scripts/*.sh
scripts/Align_fastq.sh:  $PYTHON "${PYTHON_REMOVEQC_GZ}" "$fastq1" \
scripts/Align_fastq.sh:  $PYTHON "${PYTHON_REMOVEQC_GZ}" "$fastq2" \
scripts/Align_mem.sh:  $PYTHON "${PYTHON_REMOVEQC_GZ}" "$fastq1" \
scripts/Align_mem.sh:  $PYTHON "${PYTHON_REMOVEQC_GZ}" "$fastq2" \
scripts/Germline.sh:              $PYTHON "${PYTHON_VCF_GERMLINE}" \
scripts/MutContext.sh:        $PYTHON "$WIGFIXER" "$wigfile" > "${prefix}.temp.bed" || error "Conversion failed"
scripts/MutContext.sh:        $PYTHON "$CALCULATE" \
scripts/MutDet.sh:        { time $PYTHON "$REORDER" "${prefix}.indels.annotated.vcf" \
scripts/MutDet.sh:        { time $PYTHON "${LG3_HOME}/scripts/annotation_BED_forUG.py" \
scripts/MutDet.sh:        { time $PYTHON "${LG3_HOME}/scripts/annotation_UG.py" \
scripts/MutDet.sh:        { time $PYTHON "${LG3_HOME}/scripts/annotation_COSMIC.py" \
scripts/MutDet.sh:        { time $PYTHON "${LG3_HOME}/scripts/annotation_KINASE.py" \
scripts/MutDet.sh:        { time $PYTHON "${LG3_HOME}/scripts/annotation_CANCER.py" \

where PYTHON is set as:

$ grep -F "PYTHON=" scripts/*.sh
$ grep -E "^PYTHON=" scripts/*.sh
scripts/Align_fastq.sh:PYTHON=/usr/bin/python
scripts/Align_mem.sh:PYTHON=/usr/bin/python
scripts/Germline.sh:PYTHON=/usr/bin/python
scripts/MutContext.sh:PYTHON=/opt/local/bin/python
scripts/MutDet.sh:PYTHON=/usr/bin/python

UCSF-Costello-Lab / LG3_Pipeline

CLEANUP: Set PYTHON to stable python version and use everywhere #137