return most recent genome build for the pipeline config file.
authorDiane Trout <diane@caltech.edu>
Wed, 23 Jan 2008 01:52:40 +0000 (01:52 +0000)
committerDiane Trout <diane@caltech.edu>
Wed, 23 Jan 2008 01:52:40 +0000 (01:52 +0000)
commit60581e340d01f974805ef5895ee43d441ebf66db
treeb177a1a9edb3d375d6d3313dccd2ecc9a5cfeea1
parenta11f8ed00a141c6217b258d334fa67aa30ed08e0
return most recent genome build for the pipeline config file.

Brandon's original pipeline customization code replaced things
like %(genome|build)s with the path to the ELAND genome files.

What I did is made it possible to substitute keys like %(genome)s in
addition to %(genome|build)s. The idea is that the most config files
will be set to use whatever is the "most recent" build, but hopefully
at some point we'll provide some way of specifying which build.

The way I defined "most recent" genome build was to use the
alphanum sort, that sorts mixed alpha/numeric strings in the
'natural' order instead of ASCII order, thus "mm10" > "mm8".

For the genomes that we had installed right now this would work
for everything but arabadopsis--which appears to be using a version
number of MMDDYYYY. Though if we changed it to YYYYMMDD everything
should work correctly.
gaworkflow/pipeline/genome_mapper.py
gaworkflow/pipeline/test/test_genome_mapper.py [new file with mode: 0644]
gaworkflow/util/__init__.py [new file with mode: 0644]
gaworkflow/util/alphanum.py [new file with mode: 0644]