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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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heatmap.MWAH.R has hard coded RScript path #7

Open s-andrews opened 9 years ago

s-andrews commented 9 years ago

The heatmap.MWAH.R file distributed with the program has a hardcoded path to RScript (/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript) rather than using a standard path so this fails on all external systems.

s-andrews commented 9 years ago

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 commented 9 years ago

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

s-andrews commented 9 years ago

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 commented 9 years ago

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.