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\f0\fs20 \cf2 \CocoaLigature0 #!/\cf3 \cb4 bin\cf2 \cb1 /bash\cf5 \
\cf2 #$ -l arch=linux-x64\cf5 \
\cf2 #$ -l h_rt=48:0:0\cf5 \
\cf2 #$ -l mem_free=8G\cf5 \
\cf2 #$ -S /\cf3 \cb4 bin\cf2 \cb1 /bash\cf5 \
\cf2 #$ -cwd\cf5 \
\cf2 #$ -j y\cf5 \
\cf2 #$ -r y\cf5 \
\
\cf6 export\cf7  _JAVA_OPTIONS=\cf6 "\cf8 -Xms256M -Xmx16384M -XX:ParallelGCThreads=1\cf6 "\cf5 \
\cf6 export\cf7  PATH=\cf6 "\cf8 /netapp/home/kirsty.jamieson/miniconda3/\cf9 \cb4 bin\cf8 \cb1 :\cf10 $PATH\cf6 "\cf5 \
\cf7 LIB\cf5 =/netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline\
\
\cf6 source\cf5  activate encode-atac-seq-pipeline\
\cf7 INPUT\cf5 =\cf10 $LIB\cf5 /examples/\cf6 local\cf5 /ENCSR356KRQ_subsampled.json\
java \cf10 -jar\cf5  \cf10 -Dconfig\cf5 .file\cf6 =\cf10 $LIB\cf5 /backends/backend.conf \cf10 $LIB\cf5 /cromwell-34.jar run atac.wdl \cf10 -i\cf5  \cf10 $\{INPUT\}}