From 4eb4b3b8af07370c9d86175cac348c2898da7b1d Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 6 Feb 2020 11:52:43 +0100
Subject: [PATCH] Auto load modules in bam2bigwig.sh

---
 scripts/bam2bigwig.sh | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/scripts/bam2bigwig.sh b/scripts/bam2bigwig.sh
index 45a339c..cce3a19 100755
--- a/scripts/bam2bigwig.sh
+++ b/scripts/bam2bigwig.sh
@@ -10,7 +10,7 @@
 # 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)
+# * bedops (for bedmap) -> module load bedops/2.4.36
 # * python3 -> module load Python/3.6.0
 # * samtools -> module load samtools/1.9
 # * bedtools -> module load bedtools/2.25.0
@@ -18,6 +18,16 @@
 # * parallel (for niceload) -> module load parallel/20170122
 # * UCSC-tools (for bedGraphToBigWig) -> module load UCSC-tools/v373
 
+load_tools ()
+{
+     [ bedops --version 2> /dev/null ] || module load bedops/2.4.36
+     [ python3 -V 2> /dev/null ] || module load bedops/2.4.36
+     [ samtools --version 2> /dev/null ] || module load samtools/1.9
+     [ bedtools --version 2> /dev/null ] || module load bedtools/2.25.0
+     [ niceload --version 2> /dev/null ] || module load parallel/20170122
+     [ bedGraphToBigWig 2> /dev/null ] || module load UCSC-tools/v373
+}
+
 workdir=$(mktemp -d)
 
 cleanup()
@@ -42,6 +52,8 @@ error_exit ()
 
 mawk --version 1> /dev/null 2> /dev/null || alias mawk='awk'
 
+load_tools || error_exit "Some tools are not available"
+
 bam=${1}
 bin_file=${2}
 # Example of how to generate the bin_file from iGenome data:
@@ -50,6 +62,7 @@ bin_file=${2}
 #        | sed 's/SN://g' | sed 's/LN://' \
 #        | bedops --chop 10 - \
 #        > Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed
+# A genome.dict file can be extracted from a bam file: samtools view -H <bam file>
 
 # Ensure we use a 3 columns minimal bed for bin_file:
 
-- 
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