Commit 326e2a7e authored by Blaise Li's avatar Blaise Li
Browse files

Document dependencies of bam2bigwig.sh

parent 736027d1
......@@ -9,6 +9,14 @@
# If it is a file, it should contain at least two columns,
# the first one with library names and the second with size factors.
# If it is a value, it shoud be the size factor.
# Requires:
# * bedops (for bedmap)
# * python3 -> module load Python/3.6.0
# * samtools -> module load samtools/1.9
# * bedtools -> module load bedtools/2.25.0
# * mawk -> use alias if absent
# * parallel (for niceload) -> module load parallel/20170122
# * UCSC-tools (for bedGraphToBigWig) -> module load UCSC-tools/v373
workdir=$(mktemp -d)
......@@ -32,6 +40,7 @@ error_exit ()
exit 1
}
mawk --version 1> /dev/null 2> /dev/null || alias mawk='awk'
bam=${1}
bin_file=${2}
......
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