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pipeline_driver_phospho.sh
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#!/bin/sh
# Check that the containers are available
[ ! -z $(docker images -q motrpac-prot-masic:v1.2_20200901) ] || echo "docker container < motrpac-prot-masic:v1.2_20200901 > does not exist"
[ ! -z $(docker images -q chambm/pwiz-skyline-i-agree-to-the-vendor-licenses) ] || echo "docker image < msconvert > does not exist"
[ ! -z $(docker images -q motrpac-prot-msgfplus:v1.2_20200901) ] || echo "docker container < motrpac-prot-msgfplus:v1.2_20200901 > does not exist"
[ ! -z $(docker images -q motrpac-prot-ppmerror:v1.2_20200901) ] || echo "docker container < motrpac-prot-ppmerror:v1.2_20200901 > does not exist"
[ ! -z $(docker images -q motrpac-prot-mzid2tsv:v1.2_20200901) ] || echo "docker container < motrpac-prot-mzid2tsv:v1.2_20200901 > does not exist"
[ ! -z $(docker images -q motrpac-prot-phrp:v1.2_20200901) ] || echo "docker container < motrpac-prot-phrp:v1.2_20200901 > does not exist"
[ ! -z $(docker images -q motrpac-prot-plexedpiper:v1.2_20200901) ] || echo "docker container < motrpac-prot-plexedpiper:v1.2_20200901 > does not exist"
# Step 00
docker run -v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step00:/step00:rw \
motrpac-prot-masic:v1.2_20200901 bash step00/step00masic_phospho.sh
# Step 01
docker run --rm \
-e WINEDEBUG=-all \
-v $PWD/data:/data:rw \
chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \
wine msconvert /data/test_phospho/raw/*.raw \
-o /data/test_phospho/msgfplus_input/
# Step 02
docker run \
-v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step02:/step02:rw \
motrpac-prot-msgfplus:v1.2_20200901 bash step02/step02msgfplus_tryptic_phospho.sh
# Step 03a
sh step03/step03a_phospho.sh
# Step 03b
docker run -v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step03:/step03:rw \
motrpac-prot-ppmerror:v1.2_20200901 bash step03/step03b_phospho.sh
# Step 04
docker run -v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step04:/step04:rw \
motrpac-prot-msgfplus:v1.2_20200901 bash step04/step04msgfplus_phospho.sh
# Step 05
docker run -v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step05:/step05:rw \
motrpac-prot-mzid2tsv:v1.2_20200901 bash step05/step05net462_phospho.sh
# Step 06
docker run -v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step06:/step06:rw \
motrpac-prot-phrp:v1.2_20200901 bash step06/step06phrp_phospho.sh
# Step 07
docker run -v $PWD/data:/data:rw \
-v $PWD/parameters:/parameters:rw \
-v $PWD/step07:/step07:rw \
motrpac-prot-ascore:v1.2_20200901 bash step07/step07ascore_phospho.sh
# Relative quantification step
docker run -v $PWD/data:/data:rw \
-v $PWD/relquant:/relquant:rw \
motrpac-prot-plexedpiper:v1.2_20200901 bash relquant/relquant_phospho.sh