Unverified Commit 8a8ed5f1 authored by Muhammad Saad Shamim's avatar Muhammad Saad Shamim Committed by GitHub
Browse files

Merge pull request #251 from dudcha/encode-mega 

Pull in changes for ENCODE mega
parents 7b21fd62 ca33ac47

CPU/common/diploid_split.awk

+1 −1
Changes for CPU/common/diploid_split.awk: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -28,7 +28,7 @@ 
# diff has paternal assigned to one read end and maternal assigned to the other

# mismatch has at least one SNP that doesn't match either the reference or the

# alternate

# Juicer version 1.5

# Juicer version 2.0

NF==13{

    if ($12 ~ /mismatch/ || $13 ~ /mismatch/) {

        print >> stem"mismatch.txt";

CPU/common/juicer_arrowhead.sh

+17 −1
Changes for CPU/common/juicer_arrowhead.sh: 17 added lines, 1 removed line.
Original line number Diff line number Diff line
@@ -37,7 +37,22 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

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

juicer_tools_path="/broad/aidenlab/scripts/juicer_tools"



# Aiden Lab specific check

isRice=$(hostname | awk '{if ($1~/rice/){print 1}else {print 0}}')

isBCM=$(hostname | awk '{if ($1~/bcm/){print 1}else {print 0}}')

isVoltron=0

# Set default appropriately

if [ $isRice -eq 1 ]

then

    juicer_tools_path="/projects/ea14/juicer/scripts/juicer_tools"

elif [ $isBCM -eq 1 ]

then

    juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"

else

    isVoltron=1

    juicer_tools_path="/gpfs0/juicer2/scripts/juicer_tools"

fi



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

    case $opt in
@@ -62,6 +77,7 @@ fi 


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

echo -e "ARROWHEAD:\n"

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

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

if [ $? -ne 0 ]; then

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

CPU/common/juicer_hiccups.sh

+21 −3
Changes for CPU/common/juicer_hiccups.sh: 21 added lines, 3 removed lines.
Original line number Diff line number Diff line
@@ -37,8 +37,25 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

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

juicer_tools_path="/broad/aidenlab/scripts/juicer_tools"

bed_file_dir="/broad/aidenlab/references/motif"



# Aiden Lab specific check

isRice=$(hostname | awk '{if ($1~/rice/){print 1}else {print 0}}')

isBCM=$(hostname | awk '{if ($1~/bcm/){print 1}else {print 0}}')

isVoltron=0

# Set default appropriately

if [ $isRice -eq 1 ]

then

    juicer_tools_path="/projects/ea14/juicer/scripts/juicer_tools"

    bed_file_dir="/projects/ea14/juicer/references/motif"

elif [ $isBCM -eq 1 ]

then

    juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"

    bed_file_dir="/storage/aiden/juicer/references/motif"

else

    isVoltron=1

    juicer_tools_path="/gpfs0/juicer2/scripts/juicer_tools"

    bed_file_dir="/gpfs0/juicer2/references/motif"

fi



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

    case $opt in
@@ -66,6 +83,7 @@ fi 
echo -e "\nHiCCUPS:\n"

if hash nvcc 2>/dev/null

then

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

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

    if [ $? -ne 0 ]; then

	echo "***! Problem while running HiCCUPS";
@@ -75,7 +93,7 @@ else 
    echo "GPUs are not installed so HiCCUPs cannot be run";

fi



if [ -e ${hic_file_path%.*}"_loops" ]

if [ -n "$(ls -A ${hic_file_path%.*}_loops)" ]

then

    echo -e "\nAPA:\n"

    ${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops/merged_loops.bedpe" "apa_results"

CPU/common/juicer_postprocessing.sh

+22 −5
Changes for CPU/common/juicer_postprocessing.sh: 22 added lines, 5 removed lines.
Original line number Diff line number Diff line
@@ -39,8 +39,25 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

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

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

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



# Aiden Lab specific check

isRice=$(hostname | awk '{if ($1~/rice/){print 1}else {print 0}}')

isBCM=$(hostname | awk '{if ($1~/bcm/){print 1}else {print 0}}')

isVoltron=0

# Set default appropriately

if [ $isRice -eq 1 ]

then

    juicer_tools_path="/projects/ea14/juicer/scripts/juicer_tools"

    bed_file_dir="/projects/ea14/juicer/references/motif"

elif [ $isBCM -eq 1 ]

then

    juicer_tools_path="/storage/aiden/juicer/scripts/juicer_tools"

    bed_file_dir="/storage/aiden/juicer/references/motif"

else

    isVoltron=1

    juicer_tools_path="/gpfs0/juicer2/scripts/juicer_tools"

    bed_file_dir="/gpfs0/juicer2/references/motif"

fi



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

    case $opt in
@@ -84,17 +101,17 @@ else 
    echo "GPUs are not installed so HiCCUPs cannot be run";

fi



if [ -f ${hic_file_path%.*}"_loops/merged_loops.bedpe" ]

if [ -e ${hic_file_path%.*}"_loops" ]

then

    echo -e "\nAPA:\n"

    ${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops/merged_loops.bedpe" "apa_results"

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

    ## Check that bed folder exists

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

	echo "***! Can't find folder ${bed_file_dir}";

	echo "***! Not running motif finder";

    else

	echo -e "\nMOTIF FINDER:\n"

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

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

    fi

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

else

CPU/common/juicer_tools

+3 −20
Changes for CPU/common/juicer_tools: 3 added lines, 20 removed lines.
Original line number Diff line number Diff line 
#!/bin/bash

#!/bin/bash -l

#

# Copyright (c) 2015 Aiden Lab

#
@@ -20,22 +20,5 @@ 
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

# THE SOFTWARE.

#

# Juicer 1.5

if [ "$CALLEDBY" = "AWS" ]

then

    echo "AWS"

    java -Djava.io.tmpdir=/opt/juicer/tmp -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64  -Xmx32000m -Xms8000m -jar `dirname $0`/juicer_tools.7.0.jar $*

elif [ "$CALLEDBY" = "UGER" ]

then

    echo "UGER"

    java -Djava.awt.headless=true  -Xmx16000m  -jar `dirname $0`/juicer_tools.7.5.jar  $*

elif [ "$CALLEDBY" = "SLURM" ]

then

    echo "SLURM"

    java -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Xmx16000m -Xms16000m -Xgcthreads1 -jar `dirname $0`/juicer_tools.7.5.jar $*

elif [ "$CALLEDBY" = "LSF" ] 

then

    java -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Xmx16000m -Xms16000m -Xgcthreads1 -jar `dirname $0`/juicer_tools.7.0.jar $*

else # default, don't use temp directory or gpus, use CUDA 7.0

    java -Djava.awt.headless=true  -Xmx16000m  -jar `dirname $0`/juicer_tools.jar  $*

fi
 
# Juicer version 2.0

java -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Ddevelopment=false -jar `dirname $0`/juicer_tools.jar $*

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