README.md

 # Miscellaneous things to process high throughput sequencing data.
 
-This Python package also installs a shell script depending on samtools:
-`sam2indexedbam.sh`
+This Python package also installs some shell scripts:
+
+* `sam2indexedbam.sh` (depends on samtools)
+* `bam2bigwig.sh` (depends on bedops, python3, samtools, bedtools, niceload from parallel and bedGraphToBigWig from UCSC-tools)
+
 
 ## Installing
 
@@ -11,3 +14,9 @@ It might also work directly:
 
     python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/libhts.git
 
+
+## Citing
+
+If you use this package, please cite the following paper:
+
+> Barucci et al, 2020 (doi: [10.1038/s41556-020-0462-7](https://doi.org/10.1038/s41556-020-0462-7))

scripts/bam2bigwig.sh

@@ -37,7 +37,7 @@
 load_tools ()
 {
      [ bedops --version 2> /dev/null ] || module load bedops/2.4.36
-     [ python3 -V 2> /dev/null ] || module load bedops/2.4.36
+     [ python3 -V 2> /dev/null ] || module load Python/3.7.2
      [ 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