Merge pull request #14 from rokitalab/feature/update-fragpipe-23.1

Update fragPipe to v23.1

Author: rjcorb

.gitignore

@@ -57,4 +57,3 @@ diaTracer-1.1.5.jar
 data/*
 tmp/
 
-

Dockerfile

@@ -60,8 +60,8 @@ RUN mkdir tmp
 RUN chmod 777 tmp
 
 # download and install fragPipe
-RUN wget https://github.com/Nesvilab/FragPipe/releases/download/22.0/FragPipe-22.0.zip -P fragPipe-22.0
-RUN unzip fragPipe-22.0/FragPipe-22.0.zip -d fragPipe-22.0
+RUN wget https://github.com/Nesvilab/FragPipe/releases/download/23.1/FragPipe-23.1-linux.zip -P fragPipe-23.1
+RUN unzip fragPipe-23.1/FragPipe-23.1-linux.zip -d fragPipe-23.1
 RUN chmod -R 777 /fragpipe_bin
 
 # set environment variables
@@ -70,9 +70,9 @@ 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
+COPY MSFragger-4.3.jar /fragpipe_bin/fragPipe-23.1/fragpipe/tools/MSFragger-4.3.jar 
+COPY diaTracer-1.3.3.jar /fragpipe_bin/fragPipe-23.1/fragpipe/tools/diaTracer-1.3.3.jar
+COPY IonQuant-1.11.11.jar /fragpipe_bin/fragPipe-23.1/fragpipe/tools/IonQuant-1.11.11.jar
 
 WORKDIR /rocker-build/
 

run_fragpipe.sh

@@ -5,7 +5,7 @@ set -o pipefail
 
 # Set tools and input directories
 input_dir=input
-tools_dir=/fragpipe_bin/fragPipe-22.0/fragpipe/tools
+tools_dir=/fragpipe_bin/fragPipe-23.1/fragpipe/tools
 
 # Error out if no custom.fasta is provided
 if [ ! -e "$input_dir/custom.fasta" ]; then
@@ -79,9 +79,9 @@ manifest=/home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest_sub
 fi
 
 res_dir=/home/rstudio/fragpipe/results
-tools_dir=/fragpipe_bin/fragPipe-22.0/fragpipe/tools
+tools_dir=/fragpipe_bin/fragPipe-23.1/fragpipe/tools
 
-/fragpipe_bin/fragPipe-22.0/fragpipe/bin/fragpipe --headless --workflow $wf --manifest $manifest --workdir $res_dir --config-tools-folder $tools_dir
+/fragpipe_bin/fragPipe-23.1/fragpipe/bin/fragpipe --headless --workflow $wf --manifest $manifest --workdir $res_dir --config-tools-folder $tools_dir
 
 # clear tmp directory
 rm -rf $tmp_dir/*