Commit 6999168b authored by nchernia's avatar nchernia
Browse files

Adding stages and some other checks to the mega script

parent 6ec734a0

SLURM/scripts/fragment.pl

+1 −1
Changes for SLURM/scripts/fragment.pl: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -36,7 +36,7 @@ 


use POSIX;



$site_file = "/poscratch/aidenlab/juicer/restriction_sites/hg19_DpnII.txt";

$site_file = "/projects/ea14/juicer/restriction_sites/hg19_DpnII.txt";

# Check arguments

if (scalar(@ARGV) == 2) {

  ($infile,$outfile) = @ARGV;

SLURM/scripts/fragment_4dnpairs.pl

100644 → 100755
+0 −0

File mode changed from 100644 to 100755.

View file

SLURM/scripts/juicer_arrowhead.sh

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

genomeID="hg19"

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

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

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



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

    case $opt in

SLURM/scripts/juicer_hiccups.sh

+2 −2
Changes for SLURM/scripts/juicer_hiccups.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -37,8 +37,8 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

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

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

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

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

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



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

    case $opt in

SLURM/scripts/juicer_postprocessing.sh

+2 −2
Changes for SLURM/scripts/juicer_postprocessing.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -39,8 +39,8 @@ printHelpAndExit() { 
#set defaults

genomeID="hg19"

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

juicer_tools_path="/work/ea14/juicer/juicer_tools"

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

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

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



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

    case $opt in

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