Commit e8b29eb9 authored by Aiden Lab's avatar Aiden Lab
Browse files

fixed some small issues that might have resulted in script reporting nonexistent problem

parent 518c0a1f

CPU/common/juicer_postprocessing.sh

+2 −2
Changes for CPU/common/juicer_postprocessing.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -84,10 +84,10 @@ else 
    echo "GPUs are not installed so HiCCUPs cannot be run";

fi



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

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

then

    echo -e "\nAPA:\n"

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

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

    ## Check that bed folder exists    

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

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

CPU/juicer.sh

+1 −0
Changes for CPU/juicer.sh: 1 added line, 0 removed lines.
Original line number Diff line number Diff line
@@ -594,4 +594,5 @@ then 
fi

#CHECK THAT PIPELINE WAS SUCCESSFUL

export early=$earlyexit

export splitdir=$splitdir

source ${juiceDir}/scripts/common/check.sh

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