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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