bioperl-run
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bioperl
BioPerl wrappers
I updated Phyml.pm to: - Fix issues #43 and #44. The previous commit aiming these two issues did not actually fix them; - Make it compatible to `-b (--bootstrap)` option...
Looks like `Helicobacter_pylori_26695.mod` will also do Thanks!
The [`t/Eponine.t`](https://github.com/bioperl/bioperl-run/blob/master/t/Eponine.t) test failed if Java not installed. There is an error in [line 20](https://github.com/bioperl/bioperl-run/blob/master/t/Eponine.t#L20): open(my $PIPE,"java -version 2>&1 |") || exit; If Java not installed the test just exits...
Seeing the following with recent version of bedtools: ``` 11:09 $ prove -lrv t/BEDTools.t t/BEDTools.t .. 1..423 ok 1 - make a default factory ok 2 - default to command...
The `Build.PL` script makes reference to a `Bio::Run` module that does not exist. This is the `module_name` for `Module::Build`
Hi, there is another [bug report](https://bugs.debian.org/887578) concerning bowtie tests. The error message in the build is: # Failed test 'bowtie success' # at t/Bowtie.t line 188. # '# reads processed:...
https://rt.cpan.org/Ticket/Display.html?id=56576 Also note that fasta functionality with newer versions may be broken.
Hi, there is an [issue](https://bugs.debian.org/868073) reported to the Debian bug tracker, which uncovers a problem with bowtie 1.1.2: ------------- EXCEPTION ------------- MSG: /usr/bin/bowtie call crashed: There was a problem running...
Hi, while trying to run unit tests while doing the bioperl-run Debian package I relaised that the Perl wrapper frequently calls cmscore. However, when looking at the infernal changelog of...
We use cpanm for all of our installs and it doesn't appear to be possible to build in this way. I can see that you have an alternative build method...
