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updated scrits 2 & 3 to work with bscli v2 #1

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updated scrits 2 & 3 to work with bscli v2 #1

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bf9cbbc
Update app version. Increment pipeline version. Change template scrip…
Mar 16, 2018
89f93d4
updated scrits 2 & 3 to work with bscli v2
Sep 10, 2018
54ecf8b
Merge branch '113' into 113
mbyvcm Sep 10, 2018
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9 changes: 4 additions & 5 deletions 1_CRUK.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@ cd $PBS_O_WORKDIR

#Description: BaseSpace app pipeline (Illumina paired-end). Not for use with other library preps/ experimental conditions.
#Mode: BY_SAMPLE
version="1.1.1"

version="1.1.3"

# Directory structure required for pipeline
#
Expand Down Expand Up @@ -95,9 +96,7 @@ if [ $(find .. -maxdepth 1 -mindepth 1 -type d | wc -l | sed 's/^[[:space:]]*//g
#soft link sample sheet
ln -s /data/archive/fastq/"$seqId"/SampleSheet.csv ..
#launch second pipeline script, move out one directory level, save working directory to a variable
cp 2_CRUK.sh .. && cp 3_CRUK.sh .. && cp /data/diagnostics/pipelines/"$pipelineName"/"$pipelineName"-"$pipelineVersion"/config.json .. \
&& cp /data/diagnostics/pipelines/"$pipelineName"/"$pipelineName"-"$pipelineVersion"/baseSpace.js ..
cd ..
cp 2_CRUK.sh .. && cp 3_CRUK.sh .. && cd ..
wd=$PWD
ssh transfer@cvx-gen01 "cd '$wd'; bash ./2_CRUK.sh './' '$negative' >./2_CRUK.out 2>./2_CRUK.err;"
fi
fi
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