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Update run fragpipe script to take command line args #25

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rjcorb wants to merge 11 commits into from
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Update run fragpipe script to take command line args #25

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687703e
add command line args to shell script
rjcorb Oct 9, 2025
aa198f6
add uniprot ref files
rjcorb Oct 9, 2025
2e977b8
add functionality to support cptac,hope dataset queries; update blast…
rjcorb Oct 10, 2025
c525173
rm blast filter step, add sbfs mount checks
rjcorb Dec 4, 2025
fe37630
rm uniprot files
rjcorb Dec 4, 2025
65bd484
update mount checks to be compatible with HOPE
rjcorb Dec 4, 2025
9ea6140
update fasta path in HOPE workflow file
rjcorb Dec 12, 2025
7cdd593
revert Dockerfile to Fragpipe v22.0
rjcorb Dec 12, 2025
8ed9055
Merge branch 'main' into rjcorb/24-command-line-args
rjcorb Dec 12, 2025
f7cb98f
update gene filtering from custom + canonical fasta
rjcorb Dec 16, 2025
7ad4e22
update splice event gene filtering
rjcorb Dec 16, 2025
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1 change: 1 addition & 0 deletions Dockerfile
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Expand Up @@ -78,6 +78,7 @@ ENV JAVA_HOME="/usr/lib/jvm/java-17-openjdk-amd64/"
RUN export JAVA_HOME

# copy Fragpipe dependencies

COPY MSFragger-4.1.jar /fragpipe_bin/fragPipe-22.0/fragpipe/tools/MSFragger-4.1.jar
COPY diaTracer-1.1.5.jar /fragpipe_bin/fragPipe-22.0/fragpipe/tools/diaTracer-1.1.5.jar
COPY IonQuant-1.10.27.jar /fragpipe_bin/fragPipe-22.0/fragpipe/tools/IonQuant-1.10.27.jar
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