edit] How do I submit a patch or enhancement to BioPerl?
FAQ - BioPerlWe suggest the following. Post your idea to the appropriate mailing list. If it is a really new idea consider taking us through your thought process. We'll help you tease out the necessary information such as what methods you'll want and how it can interact with other BioPerl modules. If it is a port of something you've already worked on, give us a summary of the current methods.
Related Questionsedit] What is BioPerl?
FAQ - BioPerlBioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.
Related QuestionsHow do I submit a patch to the Apache Group?
Apache Server Frequently Asked QuestionsThe Apache Group encourages patches from outside developers. There are 2 main "types" of patches: small bugfixes and general improvements. Bugfixes should be submitting using the Apache bug report page. Improvements, modifications, and additions should follow the instructions below. In general, the first course of action is to be a member of the dev@httpd.apache.org mailing list. This indicates to the Group that you are closely following the latest Apache developments.
Related QuestionsWhere and how can I submit a patch?
XenFaq - Xen WikiTo submit a patch, put it in xen-devel mailing list, as reported by Keir Fraser, in plain-text unified diff format inline in the main body or as an attachment. Also, please add If there is a bug in bugzilla report the id of the bug, but by now do not expect anything from bugzilla (see above: "Where and how can i report a bug?").
Related QuestionsHow should I use the male enhancement patch?
Penis Enlargement and Enhancement Products FAQ and moreAlthough this differs by product, in most cases, simply apply the patch to clean skin in the lower abdomen area, on your arm, on your inner thigh, or on the buttocks. The transdermal technology does the rest! Each patch is usually good for up to 72hrs, though it's a good idea to move them to a different location every 24 hours.
Related Questionsedit] What are the license terms for BioPerl?
FAQ - BioPerlBioPerl is licensed under the same terms as Perl itself which is the Perl Artistic License (see http://www.perl.com/pub/a/language/misc/Artistic.html or http://www.opensource.org/licenses/artistic-license.html).
Related Questionsedit] How do I run BLAST from within BioPerl?
FAQ - BioPerlUse the module Bio::Tools::Run::StandAloneBlast. It will give you access to many of the search tools in the NCBI BLAST suite including blastall, bl2seq, blastpgp. The basic structure is like this.
Related Questionsedit] What is bioperl-ext?
FAQ - BioPerlbioperl-ext is a package of code for C-extensions (hence the 'ext') to BioPerl. These include interfacing to the staden IO library (the io_lib library) for reading in chromatogram files and Bio::Ext::Align which is a Smith-Waterman implementation.
Related Questionsedit] What is bioperl-microarray?
FAQ - BioPerlThe Microarray package provides some basic tools for microarray functionality. It was started by Allen Day and may need some more work before it is a mature product.
Related Questionsedit] What is bioperl-gui?
FAQ - BioPerlThe GUI package provides a Graphical User Interface for interacting with sequence and feature objects. It is used as part of the Genquire project.
Related Questionsedit] What is bioperl-pedigree?
FAQ - BioPerlThe Pedigree package was started by Jason Stajich and provides basic tools for interacting with pedigree data and rendering pedigree plots.
Related Questionsedit] What is a patch?
Linux-NTFS FAQ - LQWikiA patch is a set of changes for a set of text files. Since we are only altering the NTFS code, it is inefficient to release all the kernel code every time we make a small change. We make our patches against official Linux kernel releases. Once you have unpacked the source, change directory into the source directory and use the command (replacing the path and patchname as necessary): This will modify the source code. There should be no rejects or failures. Next build the kernel as normal.
Related QuestionsHow do I submit a patch for Subversion?
subversion: Subversion FAQOnce you've digested that, send a mail to the dev list with the word [PATCH] and a one-line description in the subject, and include the patch inline in your mail (unless your MUA munges it up totally). Then a committer will pick it up, apply it (making any formatting or content changes necessary), and check it in. The basic process looks like this: $ svn co http://svn.collab.net/repos/svn/trunk subversion $ cd subversion/www [ make changes to faq.html ] $ svn diff faq.
Related Questionsedit] How can I tell what version of BioPerl is installed?
FAQ - BioPerlWe have a universal version number for a release. This is set in the module Bio::Root::Version which is universally applied to every module which inherits from Bio::Root::RootI. To check the version, just use the following one liner: perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' Now when we use version tuples that are not just decimal numbers, Perl converts these silently to Unicode representations.
Related QuestionsCan I edit my application once I submit it?
FAQ - Frequently Asked QuestionsNo. Before you submit an application, please ensure all of the information in your profile is updated, thorough and complete. If you withdraw the application, you can then update the information in the profile. If you resubmit the application (which must be before the closing date), it will contain the updated/revised information.
Related QuestionsOpenDX - FAQWe encourage patches from developers. There are two main "types" of patches: small bugfixes and general improvements. In general, the first course of action is to become a member of the opendx-dev@watson.ibm.com mailing list. This indicates to the group that you are closely following the latest OpenDX developments. Your patch file should be generated using either 'diff -c' or 'diff -u' against the most recent tarball. To submit your patch, send email to gabra@us.ibm.Related Questions
What is BioPerl?
BioPerl FAQ (Frequently Asked Questions)BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.
Related QuestionsHow do I submit an enhancement request?
Technesis Customer Support FAQa valued customer of Technesis, we welcome any suggestions you may have regarding enhancements to the products. All suggestions are recorded in our case tracking system following the reporting procedures outlined above and are then passed to the appropriate Product Marketing Manager. The Product Development Team will then review it during the process of planning the content of future product releases to determine whether the suggestion will be incorporated.
Related QuestionsServices: Support - FAQsa valued customer of Pilot, we welcome any suggestions you may have regarding enhancements to the products. All suggestions are recorded in our call tracking system following the reporting procedures outlined above and are then passed to the appropriate Product Marketing Manager. The Product Development Team will then review it during the process of planning the content of future product releases to determine whether the suggestion will be incorporated.Related Questions
How do I submit a suggestion or enhancement request?
Xign.netWe welcome all of your suggestions and enhancement requests. Click here to access our suggestion/enhancement request form.
Related Questionsedit] Can I query MEDLINE or other bibliographic repositories using BioPerl?
FAQ - BioPerlYes! The solution lies in Bio::Biblio*, a set of modules that provide access to MEDLINE and OpenBQS-compliant servers using SOAP. See Bio::Biblio, Bio::DB::BiblioI, scripts/biblio.PLS, or examples/biblio/* for details and example code.
Related Questionsedit] What does the future hold for running applications within BioPerl?
FAQ - BioPerlWe are trying to build a standard starting point for analysis application which will probably look like Bio::Tools::Run::AnalysisFactory which will allow the user to request which type of remote or local server they want to use to run their analyses. This will connect to the Pasteur's PISE server, the EBI's Novella server, as well as be aware of wrappers to run applications locally. Additionally we suggest investigating the BioPipe project, also known as bioperl-pipeline, at http://www.biopipe.
Related Questionsedit] bioperl-ext won't compile the staden IO lib part - what do I do?
FAQ - BioPerlAre you sure io_lib is installed where you think it is, and that the install path is seen by Perl (did you answer the questions during perl Makefile.PL ?)
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