BioPerl has switched (as of mid-April, 2014) to GitHub Issues. We still have access to the Redmine-based tracking system, but this will be effectively read-only. We no longer support access to the original Bugzilla instance.
Please submit bugs or enhancement requests to BioPerl GitHub Issues. The older BioPerl Redmine tracking system remains but is will no longer be used, and the oldest Bugzilla-based system is not supported and addition of new bugs has been disabled.
We really do want you to submit bugs, even though it means more things for us to do! It means there is something we didn't think of or test in the particular module and we won't know about this unless you tell us. The Redmine system requires you register to avoid spam and to allow us to contact you again when the bug is fixed or to clarify the problem and solutions.
It is important that you record the version of BioPerl you are running (if you don't know, see the FAQ the question is addressed there). You can also include the version of Perl you are using and the Operating System you are running.
When submitting new bugs on BioPerl on GitHub, enter a brief description and other general information. You can use Markdown to add links, syntax highlighting, and so on; see the GitHub Markdown docs for more.
You can paste example code in the description, but we suggest submitting as a GitHub Gist. If you have example fixes, we highly suggest using the tools GitHub has in place, namely the ability to fork the code and create a pull request with the relevant fix. This will show up as an issue automatically, so there isn't a need to file one separately.
Note that attachments on GitHub issues only work for images. If the example is a text file then use a GitHub Gist; alternatively, if the file is something available publicly then please provide a link to the file.
We gladly welcome patches. Patches for bioperl code should be created as described in the SubmitPatch HOWTO. Try to ensure the patch is derived against the latest code checked out from Git, particularly if the patch is large.
Briefly, you can generate the patch using the following command:
diff -u old new
For best results, follow this example:
cd $YOUR_WORKING_DIST_DIRECTORY/Bio/Frobnicator git pull git diff GrokFrobnicator.pm > my-patch.dif
Submitting New Modules and Code Snippets
We also accept new code, either as full-fledged modules or as snippets of code (snippets work better as a patch). New code must include documentation, example code (typically listed in a SYNOPSIS section), and tests with decent test coverage following our testing standards in our Writing_BioPerl_Tests HOWTO). Because we are moving to a more modular scheme for future Bioperl installations we highly suggest individual submission of modules to CPAN, primarily to help lower the barrier to submitting bug fixes.
Good bug reports are ones which provide a small amount of code and the necessary test files to reproduce your bug. By doing this work up front you insure the developer spends most of his or her time actually working on the problem. Pasting your entire 600 line program into the comment buffer is probably not going to get an enthusiastic response. In addition, isolating the problem down to a small amount of your code will help ensure that the bug is not on your end before we dive in and start working on it.
Open Issues (GitHub)
This list details the open Bugs on GitHub for BioPerl.
- Issue 78: Can't query website: 500 Can't connect to www.ncbi.nih.gov:80 (Bad hostname)
- I get this error: Can't query website: 500 Can't connect to www.ncbi.nih.gov:80 (Bad hostname) .. STACK: Bio::DB:Taxonomy::entrez::get_taxonids /usr/share/perl5/Bio/DB/Taxonomy/entrez.pm:472 when trying to use the get_Taxonomy_node() method from Bio::DB::Taxonomy. When I modified the value of $EntrezLocation in entrez.pm file line 472 from 'http://www.ncbi.niv.gov/entrez/eutils/' to 'http://www.ncbi.nlm.niv.gov/entrez/eutils/' (added the nlm subdomain) it then seems to work fine. I guess ncbi changed its url or something?
- Issue 76: $[some feature object] -> seq; throws a fatal error in the case of a gene that wraps around the ends of a linearized chromosome
- In the linear representation of a circular chromosome, sometimes a gene wraps around the ends of the numbering and therefore is annotated with coordinates like join(2006035..2007700,1..257) I noticed this error when working with accession number NC_008309.1 In this case, even a simple $[feature] -> seq will give a fatal error MSG: start  is greater than end . If you want to truncated and reverse complement, you must call trunc followed by revcom. Sorry. STACK Bio::PrimarySeqI::trunc /usr/local/share/perl/5.14.2/Bio/PrimarySeqI.pm:456 STACK Bio::SeqFeature::Generic::seq /usr/local/share/perl/5.14.2/Bio/SeqFeature/Generic.pm:705 Additionally, attempting to skip this case by checking (location -> start) > (location -> end) doesn't work, because start and end are given as 1 and 2007700 respectively. I was able to find a workaround in my specific case, but the fix is somewhat of an inelegant hack, and this probably should be fixed on the side of the module itself.
- Issue 70: CONTIG lines in GenBank files
- Per the mail list: http://lists.open-bio.org/pipermail/bioperl-l/2014-May/071579.html Example file: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptomyces_avermitilis_MA_4680_uid57739/NC_004719.gbk
- Issue 61: new modules Bio::Tools::Alignment::Overview and Bio::DB::NextProt
- Some time ago I made the mistake of uploading to CPAN a module called Bio::Tools::Alignment::Overview, the module wasn't associated to bioperl but for some reason I decided to use the namespace anyway (yeah, I know...) Now I'm organizing some projects and I decided to include the module to bioperl, so if you accept this pull request I will remove from PAUSE/CPAN the current module, so that you can upload it under bioperl. Sorry for the noobish mistake =) Cheers.
- Issue 46: Simplealign
- Hi, Chris, This is my implementation of Bio::SimpleAlign. I have a detailed report describing the improvement to the code, and explaining the failed tests using t/Align/SimpleAlign.t. If you need any help, please just let me know. Cheers, Jun