descriptionBioPerl core
homepage URLhttp://bioperl.org
repository URLgit://github.com/bioperl/bioperl-live.git
ownercjfields@bioperl.org
last changeWed, 20 Jul 2016 14:59:00 +0000 (20 09:59 -0500)
last refreshSat, 30 Jul 2016 05:26:15 +0000 (30 07:26 +0200)
content tags
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readme

Build Status Coverage Status DOI Documentation Status

Getting Started

Please see the the INSTALL or INSTALL.WIN documents for installation instructions.

About BioPerl

BioPerl is a package of public domain Perl tools for computational molecular biology.

Our website (http://bioperl.org/) provides an online resource of modules, scripts, and web links for developers of Perl-based software for life science research.

Contact Information

Please submit bugs, in particular about documentation which you think is unclear, or about problems in installation. We are also very interested in functions which don't work the way you think they do!

The Directory Structure

The BioPerl directory structure is organized as follows:

Documentation

For documentation on BioPerl see the HOWTO documents online at http://bioperl.org/howtos.

Useful documentation in the form of example code can also be found in the examples/ and scripts/ directories. The current collection includes scripts that run BLAST, index flat files, parse PDB structure files, make primers, retrieve ESTs based on tissue, align protein to nucleotide sequence, run GENSCAN on multiple sequences, and much more! See bioscripts.pod for a complete listing.

Individual *.pm modules have their own embedded POD documentation as well. A complete set of hyperlinked POD, or module, documentation is available at http://www.bioperl.org/.

Remember that 'perldoc' is your friend. You can use it to read any file containing POD formatted documentation without needing any type of translator (e.g. 'perldoc Bio::SeqIO').

If you used the Build.PL installation, and depending on your platform, you may have documentation installed as man pages, which can be accessed in the usual way.

Releases

BioPerl releases are always available from the website at http://www.bioperl.org/DIST or in CPAN. The latest code can be found at https://github.com/bioperl.

From the 1.0 release until the 1.6 release even numbers (e.g. 1.4) indicated stable releases. Stable releases were well tested and recommended for most uses. Odd numbers (e.g. 1.3) were development releases which one would only use if one were interested in the latest features. The final number (e.g. in 1.2.1) is the point or patch release. The higher the number the more bug fixes has been incorporated. In theory you can upgrade from one point or patch release to the next with no changes to your own code (for production cases, obviously check things out carefully before you switch over).

The upcoming 1.7 release will be the last release series to utilize the alternating 'stable'/'developer' convention. Starting immediately after the final 1.6 branch, we will start splitting BioPerl into several smaller easier-to-manage distributions. These will have independent versions, all likely starting with v1.7.0. We do not anticipate major API changes in the 1.7.x release series, merely that the code will be restructured in a way to make maintenance more feasible. We anticipate retaining semantic versioning until the 2.x release.

Caveats and Warnings

When you run the tests with ./Build test some tests may issue warnings messages or even fail. Sometimes this is because we didn't have anyone to test the test system on the combination of your operating system, version of perl, and associated libraries and other modules. Because BioPerl depends on several outside libraries we may not be able to test every single combination so if there are warnings you may find that the package is still perfectly useful.

If you install the bioperl-run system and run tests when you don't have the program installed you'll get messages like program XXX not found, skipping tests. That's okay, BioPerl is doing what it is supposed to do. If you wanted to run the program you'd need to install it first.

Not all scripts in the examples/ directory are correct and up-to-date. If you find an issue with a script please submit a bug report to https://github.com/bioperl/bioperl-live/issues and consider helping out in their maintenance.

If you are confused about what modules are appropriate when you try and solve a particular issue in bioinformatics we urge you to look at HOWTO documents first.

A simple module summary

Here is a quick summary of many of the useful modules and how the toolkit is laid out:

All modules are in the Bio/ namespace,

Upgrading from an older version

If you have a previously installed version of BioPerl on your system some of these notes may help you.

shortlog
9 days ago Chris FieldsMerge pull request #186 from bioperl/docker-installmaster
11 days ago Hilmar LappAdds instructions for installing BioPerl as a Docker... 186/head
11 days ago Chris FieldsMerge pull request #185 from elucify/ncbi-https
11 days ago Chris FieldsMerge pull request #181 from bioperl/limit-dockerhub...
11 days ago mjohnsonmissed one url185/head
11 days ago mjohnsonUpdated http URLs to https
13 days ago Chris Fieldsbump RCrelease-1-7-0-RC5
13 days ago Chris Fieldsrequires a newer (but still old) perl
13 days ago Chris Fieldsupdate Changes (first of a few)
2016-07-12 Hilmar LappAdds comments so it is clearer what is going on.limit-dockerhub-trigger181/head
2016-07-12 Hilmar LappExcludes branches other than master.
2016-07-12 Chris FieldsMerge pull request #179 from christiam/master
2016-07-12 Christiam CamachoChange BLAST URL to https179/head
2016-07-11 Chris FieldsRT 103272 - fix for deleting features that have decimals
2016-07-11 Chris FieldsIncorporate recommended fix for RT98374; notably tests...
2016-07-11 Chris Fieldsadd some tests for RT ticket, not a true bug but indica...
...
tags
13 days ago release-1-7-0-RC5
3 weeks ago release-1-7-0-RC4
18 months ago release-1-6-zenodo
2 years ago release-1-6-924 Minor release to deal with META...
2 years ago release-1-6-923 Latest release, with several bug...
2 years ago release-1-6-922
2 years ago release-1-6-921
2 years ago release-1-6-920
2 years ago release-1-6-910 Point release, mainly bug fixes
5 years ago bioperl-release-1-6-901
5 years ago bioperl-release-1-6-9 BioPerl core 1.6.9 release
6 years ago bioperl-release-1-6-1
6 years ago bioperl-1-6-0_006
6 years ago bioperl-1-6-0_005
6 years ago bioperl-1-6-0_003
6 years ago bioperl-1-6-0_004
...
heads
9 days ago master
11 days ago topic/phyloxml_output_refac
2 weeks ago limit-dockerhub-trigger
6 months ago v1.6.x
16 months ago topic/taxdb-to-sqlite2
17 months ago topic/rework-db-taxonomy
2 years ago topic/local_build
2 years ago topic/sf_lite_fixes
2 years ago topic/cjfields_psl_fixes
2 years ago topic/assembly-less
2 years ago topic/yinjun111-simplealign
3 years ago storable_db
3 years ago topic/tree_api_refresh
4 years ago reorganization_2.x
4 years ago topic/gsoc_2010
4 years ago topic/most_testiest
...