Commit bfe7bf89 authored by nchernia's avatar nchernia
Browse files

changed the name from juicebox to juicer_tools everywhere. deleted jars, these... 

changed the name from juicebox to juicer_tools everywhere. deleted jars, these should be downloaded from the Download page to ensure everyone has the latest copies
parent a219594d

AWS/scripts/juicebox_tools.7.0.jar

deleted100644 → 0
−32.5 MiB

File deleted.

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AWS/scripts/juicer.sh

+2 −2
Changes for AWS/scripts/juicer.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -781,7 +781,7 @@ then 
        echo "(-: Alignment and merge done, launching other jobs."

        $execstring

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${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/juicer_tools 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}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicer_tools pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; else ${juiceDir}/scripts/juicer_tools 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]" $waitstring22 -J "${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/juicer_tools 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/juicer_tools 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) \""
@@ -797,7 +797,7 @@ DOSTAT 
    #BSUB -o $topDir/lsf.out

    ${waitstring3}

    #BSUB -J "${groupname}_postproc_wrap"

    bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring4 -J "${groupname}_postproc" "${juiceDir}/scripts/juicer_postprocessing.sh -j ${juiceDir}/scripts/juicebox -i ${outputdir}/inter_30.hic -m ${juiceDir}/references/motif -g ${genomeID}"

    bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring4 -J "${groupname}_postproc" "${juiceDir}/scripts/juicer_postprocessing.sh -j ${juiceDir}/scripts/juicer_tools -i ${outputdir}/inter_30.hic -m ${juiceDir}/references/motif -g ${genomeID}"

POSTPROC

    ## LSF users change queue below to $queue

    bsub <<- FINCLN1

AWS/scripts/juicer_arrowhead.sh

+8 −8
Changes for AWS/scripts/juicer_arrowhead.sh: 8 added lines, 8 removed lines.
Original line number Diff line number Diff line
@@ -26,7 +26,7 @@ 
# This will find contact domains with Arrowhead.



## Read arguments

usageHelp="Usage: ${0} [-h] -j <juicebox_file_path> -i <hic_file_path>"

usageHelp="Usage: ${0} [-h] -j <juicer_tools_file_path> -i <hic_file_path>"



printHelpAndExit() {

    echo "$usageHelp"
@@ -36,20 +36,20 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

hic_file_path="$(pwd)/aligned/inter_30.hic"

juiceboxpath="/opt/juicer/scripts/juicer_tools"

juicer_tools_path="/opt/juicer/scripts/juicer_tools"



while getopts "h:j:i:" opt; do

    case $opt in

	h) printHelpAndExit 0;;

	j) juiceboxpath=$OPTARG ;;

	j) juicer_tools_path=$OPTARG ;;

	i) hic_file_path=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done



## Check that juicebox exists 

if [ ! -e "${juiceboxpath}" ]; then

  echo "***! Can't find juicebox in ${juiceboxpath}";

## Check that juicer tools exists 

if [ ! -e "${juicer_tools_path}" ]; then

  echo "***! Can't find juicer tools in ${juicer_tools_path}";

  exit 100;

fi
@@ -59,9 +59,9 @@ if [ ! -e "${hic_file_path}" ]; then 
  exit 100;

fi



echo -e "${juiceboxpath} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"

echo -e "${juicer_tools_path} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"

echo -e "ARROWHEAD:\n"

${juiceboxpath} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"

${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"

if [ $? -ne 0 ]; then

    echo "***! Problem while running Arrowhead";

    exit 100

AWS/scripts/juicer_hiccups.sh

+10 −10
Changes for AWS/scripts/juicer_hiccups.sh: 10 added lines, 10 removed lines.
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ 
# loops with HiCCUPS and inding motifs of these loops with MotifFinder.



## Read arguments

usageHelp="Usage: ${0} [-h] -j <juicebox_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>"

usageHelp="Usage: ${0} [-h] -j <juicer_tools_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>"



printHelpAndExit() {

    echo "$usageHelp"
@@ -37,13 +37,13 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

hic_file_path="$(pwd)/aligned/inter_30.hic"

juiceboxpath="/opt/juicer/scripts/juicer_tools"

juicer_tools_path="/opt/juicer/scripts/juicer_tools"

bed_file_dir="/opt/juicer/references/motif"



while getopts "h:g:j:i:m:" opt; do

    case $opt in

	h) printHelpAndExit 0;;

	j) juiceboxpath=$OPTARG ;;

	j) juicer_tools_path=$OPTARG ;;

	i) hic_file_path=$OPTARG ;;

	m) bed_file_dir=$OPTARG ;; 

	g) genomeID=$OPTARG ;;
@@ -51,9 +51,9 @@ while getopts "h:g:j:i:m:" opt; do 
    esac

done



## Check that juicebox exists 

if [ ! -e "${juiceboxpath}" ]; then

  echo "***! Can't find juicebox in ${juiceboxpath}";

## Check that juicer_tools exists 

if [ ! -e "${juicer_tools_path}" ]; then

  echo "***! Can't find juicer tools in ${juicer_tools_path}";

  exit 100;

fi
@@ -70,7 +70,7 @@ if [ ! -e "${bed_file_dir}" ]; then 
fi



echo -e "\nHiCCUPS:\n"

${juiceboxpath} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"

${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"

if [ $? -ne 0 ]; then

    echo "***! Problem while running HiCCUPS";

    exit 100
@@ -79,12 +79,12 @@ fi 
if [ -f ${hic_file_path%.*}"_loops.txt" ]

then

    echo -e "\nAPA:\n"

    ${juiceboxpath} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"

    ${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"

    echo -e "\nMOTIF FINDER:\n"

    ${juiceboxpath} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"

    ${juicer_tools_path} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"

    echo -e "\n(-: Feature annotation successfully completed (-:"

else

    # if loop lists do not exist but Juicebox didn't return an error, likely 

    # if loop lists do not exist but Juicer tools didn't return an error, likely 

    # too sparse

    echo -e "\n(-: Postprocessing successfully completed, maps too sparse to annotate (-:"

fi

AWS/scripts/juicer_postprocessing.sh

+12 −12
Changes for AWS/scripts/juicer_postprocessing.sh: 12 added lines, 12 removed lines.
Original line number Diff line number Diff line
@@ -29,7 +29,7 @@ 
# Juicer version 1.5



## Read arguments

usageHelp="Usage: ${0} [-h] -j <juicebox_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>"

usageHelp="Usage: ${0} [-h] -j <juicer_tools_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>"



printHelpAndExit() {

    echo "$usageHelp"
@@ -39,13 +39,13 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

hic_file_path="$(pwd)/aligned/inter_30.hic"

juiceboxpath="/opt/juicer/scripts/juicebox"

juicer_tools_path="/opt/juicer/scripts/juicer_tools"

bed_file_dir="/opt/juicer/references/motif"



while getopts "h:g:j:i:m:" opt; do

    case $opt in

	h) printHelpAndExit 0;;

	j) juiceboxpath=$OPTARG ;;

	j) juicer_tools_path=$OPTARG ;;

	i) hic_file_path=$OPTARG ;;

	m) bed_file_dir=$OPTARG ;; 

	g) genomeID=$OPTARG ;;
@@ -53,9 +53,9 @@ while getopts "h:g:j:i:m:" opt; do 
    esac

done



## Check that juicebox exists 

if [ ! -e "${juiceboxpath}" ]; then

    echo "***! Can't find juicebox in ${juiceboxpath}";

## Check that juicer_tools exists 

if [ ! -e "${juicer_tools_path}" ]; then

    echo "***! Can't find juicer tools in ${juicer_tools_path}";

    exit 100;

fi
@@ -71,9 +71,9 @@ if [ ! -e "${bed_file_dir}" ]; then 
    exit 100;

fi



echo -e "${juiceboxpath} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"

echo -e "${juicer_tools_path} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"

echo -e "ARROWHEAD:\n"

${juiceboxpath} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"

${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"

if [ $? -ne 0 ]; then

    echo "***! Problem while running Arrowhead";

    exit 100
@@ -81,7 +81,7 @@ fi 
echo -e "\nHiCCUPS:\n"

if hash nvcc 2>/dev/null 

then 

    ${juiceboxpath} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"

    ${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"

    if [ $? -ne 0 ]; then

	echo "***! Problem while running HiCCUPS";

	exit 100
@@ -93,12 +93,12 @@ fi 
if [ -f ${hic_file_path%.*}"_loops.txt" ]

then

    echo -e "\nAPA:\n"

    ${juiceboxpath} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"

    ${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"

    echo -e "\nMOTIF FINDER:\n"

    ${juiceboxpath} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"

    ${juicer_tools_path} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"

    echo -e "\n(-: Feature annotation successfully completed (-:"

else

  # if loop lists do not exist but Juicebox didn't return an error, likely 

  # if loop lists do not exist but Juicer Tools didn't return an error, likely 

  # too sparse

    echo -e "\n(-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-:"

fi

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