heatmap.MWAH.R has hard coded RScript path

[shendurelab]

heatmap.MWAH.R has hard coded RScript path

[s-andrews]

The same bug is in lots of other places:

$ grep vol3 *
CountMappables.pl:#!/net/gs/vol3/software/modules-sw/perl/5.14.2/Linux/RHEL6/x86_64/bin/perl -w
CreateScaffoldedFasta.pl:#!/net/gs/vol3/software/modules-sw/perl/5.14.2/Linux/RHEL6/x86_64/bin/perl -w
heatmap.R:#!/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript
PreprocessSAMs.pl:my $samtools = '/net/gs/vol3/software/modules-sw/samtools/0.1.18/Linux/RHEL6/x86_64/bin/samtools';
QuickDotplot:#!/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript
QuickDotplot~:#!/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript
QuickDotplot.POA.R:#!/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript
QuickDotplot.SKY.R:#!/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript

[s-andrews]

PreprocessSAMs.pl also has hard coded paths to make_bed_around_RE_site.pl, bedtools and samtools.

[s-andrews]

QuickDotplot.SKY.R has hard coded input files from ~/vol10/src something and ~/public_html

I'm not sure how much I want to chase this any more since it's obvious that whoever reviewed this didn't even try to confirm that it ran.

[cwbeitel]

In your development you guys should probably make use of a test system that allows you to test against multiple environments like tox+circleci is for python.