I noticed that the instructions at
https://wiki.galaxyproject.org/Admin/DataIntegration direct admins to
update the builds.txt file when adding a new reference genome to local
Galaxy instances. Up to this point I had been actually modifying the
manual_builds.txt file and then rebuilding the builds.txt file using the
updateucsc.sh script. This allows me to continue to use the
updateuscs.sh script without overwriting my changes and also generates a
BUILD.len file in the chrom/ directory. It does require some scripting
since one needs to add the chromosome lengths to manual_builds.txt, but
this is relatively straight forward using an indexed fasta file (.fai)
or similar. Perhaps a larger issue is that the manual_builds.txt file
is currently under source control in mercurial (instead of being
generated by a .sample version).
So I have two questions:
1) What would be "best practice" for adding a new genome? Updating
builds.txt or manual_builds.txt?
2) Can the manual_builds.txt file be generated from a sample and moved
out of source control? (I'll add a Trello card if this seems reasonable).
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/