Adding Reference Genomes, builds.txt vs manual_builds.txt

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Adding Reference Genomes, builds.txt vs manual_builds.txt

Lance Parsons
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

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