I've run into one bug and a one other smaller issue with the Tophat2
wrapper.
The bug manifests itself when running the tool with "use Defaults"
selected results in the following error:
cp: cannot stat
`/data/galaxy-dev/galaxy-dev/database/job_working_directory/000/281/tophat_out/fusions.out':
No such file or directory
It seems that somehow, the filter on the output dataset is not working
properly when the value (params['fusion_search']['do_search']) is not
explicitly set in the parameters.
The second issue is more minor. It seems that the Tophat2 wrapper
assumes that Tophat2 will use Bowtie2 (and not Bowtie). However, the
actual Tophat2 program will only use Bowtie2 if it is found in the
path. Otherwise it defaults to using bowtie which results in an error
(Could not find Bowtie index files) since the wrapper points the tool to
the bowtie2 index instead. To make things a bit more robust, I suggest
adding bowtie2 as a requirement to the tophat2 wrapper. It also might
be a good idea to add versions to those requirements. I've attached a
small patch to do that (though it's fairly trivial).
Thanks.
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
--- tophat2_wrapper.xml 2012-09-12 11:41:46.000000000 -0400
+++ tophat2_wrapper_withreqs.xml 2012-09-14 13:23:25.000000000 -0400
@@ -3,7 +3,8 @@
<description>Gapped-read mapper for RNA-seq data</description>
<version_command>tophat2 --version</version_command>
<requirements>
- <requirement type="package">tophat2</requirement>
+ <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
+ <requirement type="package" version="2.0.4">tophat2</requirement>
</requirements>
<command interpreter="python">
tophat2_wrapper.py
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