Commit 3fb9f25f authored by nchernia's avatar nchernia
Browse files

small change to echo in the Experiment description so that newlines are handled correctly

parent 1c414dde

AWS/scripts/juicer.sh

+2 −2
Original line number Diff line number Diff line
@@ -779,9 +779,9 @@ then 
        #BSUB -J "${groupname}_launch"

        echo "(-: Alignment and merge done, launching other jobs."

        bkill -J ${groupname}_clean2

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_rmsplit) && done(${groupname}_osplit)" -J "${groupname}_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_rmsplit) && done(${groupname}_osplit)" -J "${groupname}_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_rmsplit) && done(${groupname}_osplit)" -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; fi"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_rmsplit) && done(${groupname}_osplit)" -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; fi"

DOSTAT

	waitstring3="#BSUB -w \" done(${groupname}_launch) \""

	waitstring4="-w \"done(${groupname}_hic30)\""

UGER/scripts/juicer.sh

+2 −2
Original line number Diff line number Diff line
@@ -689,13 +689,13 @@ then 
        source $usePath

        $load_cluster

        qsub -o $topDir/uger.out -q $long_queue -l m_mem_free=16g -N ${groupname}_stats -j y -r y $holdjobs <<- EOF  

source $usePath; $load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt

source $usePath; $load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt

EOF

        qsub -o $topDir/uger.out -q $long_queue -l m_mem_free=16g -N ${groupname}_hic -hold_jid ${groupname}_stats -j y -r y <<- EOF 

        source $usePath; $load_java; export _JAVA_OPTIONS=-Xmx16384m; if [ -n "$nofrag" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;

EOF

 	qsub -o $topDir/uger.out -q $long_queue -l m_mem_free=16g -N ${groupname}_hic30 -j y -r y $holdjobs <<- EOF 

source $usePath; $load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n "$nofrag" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; fi

source $usePath; $load_java; export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n "$nofrag" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; fi

EOF

DOSTAT

    fi

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