Make slurm-compatible script.

scripts/bam2bigwig.sh

-#!/bin/dash
+#!/bin/bash -l
 # Usage: bam2bigwig.sh <sorted.bam> <bin_file> <library_name> <orientation> <strandedness> [<normalization>] <bigwig>
 # <bin_file> should be a bed file representing 10 bp bins along the genome
 # <orientation> must be "all", "fwd" or "rev"
@@ -30,7 +30,6 @@
 # * 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
 
@@ -66,7 +65,6 @@ error_exit ()
     exit 1
 }
 
-mawk --version 1> /dev/null 2> /dev/null || alias mawk='awk'
 
 load_tools || error_exit "Some tools are not available"
 
@@ -74,7 +72,7 @@ bam=${1}
 bin_file=${2}
 # Example of how to generate the bin_file from iGenome data:
 #    cd /Genomes/C_elegans
-#    mawk '$1 == "@SQ" {print $2"\t0\t"$3}' Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.dict \
+#    awk '$1 == "@SQ" {print $2"\t0\t"$3}' Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.dict \
 #        | sed 's/SN://g' | sed 's/LN://' \
 #        | bedops --chop 10 - \
 #        > Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed
@@ -163,7 +161,7 @@ fi
 echo "getting chromosome bounds"
 genome_file="${workdir}/chrom_sizes.txt"
 samtools view -H ${bam} \
-    | mawk '$1 == "@SQ" {print $2"\t"$3}' \
+    | awk '$1 == "@SQ" {print $2"\t"$3}' \
     | sed 's/SN://g' | sed 's/LN://' \
     > ${genome_file} || error_exit "making ${genome_file} failed"
     #> ${genome_file} || cleanup && error_exit "making ${genome_file} failed"
@@ -172,7 +170,7 @@ compute_coverage()
 {
     cmd="niceload --noswap bedtools genomecov -bg -split ${orient_filter} ${scaling} -ibam ${bam}"
     eval ${cmd} \
-        | mawk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \
+        | awk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \
         || error_exit "compute_coverage failed"
         #|| cleanup && error_exit "compute_coverage failed"
 }