adding a new ensemble genome build

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

adding a new ensemble genome build

Nikolay N.

I am a galaxy newbie so apologise if the questions appears trivial.

I installed an instance locally and would like to add the most recent Ensemble mouse genome build ( which is referred to using a confusing multitude of identifiers (this rant is not related to galaxy), among others GRCm38 (GCA_000001635.3), GRCm38.p1 and Ensemble mus musculis build 71. 

I wanted to add a record for this genome build in /home/nikolay/galaxy/galaxy-dist/tool-data/shared/ensembl/builds.txt. This file seems to have a tabular format and there are already some mouse records there:

MGSC1 67 Mus_musculus (Mouse/MGSC1)
MGSC3 67 Mus_musculus (Mouse/MGSC3)
NCBIM30 67 Mus_musculus (Mouse/NCBIM30)
NCBIM32 67 Mus_musculus (Mouse/NCBIM32)
NCBIM33 67 Mus_musculus (Mouse/NCBIM33)
NCBIM34 67 Mus_musculus (Mouse/NCBIM34)
NCBIM35 67 Mus_musculus (Mouse/NCBIM35)
NCBIM36 67 Mus_musculus (Mouse/NCBIM36)
NCBIM37 67 Mus_musculus (Mouse/NCBIM37)

But none of these records contains an id that bears any resemblance to the ids used by Ensemble. How do you guys come up with the ids for these genome builds? Is there any convention that I shall follow? Also, I find it a bit confusing that there is a numeric build id as well. It seems to be the same for all records. Does it have any role? (I assume not as it does not make sense to have the same id for all records). It would be really helpful if you can explain a bit more about the format/convention used in ensemble/builds.txt - if there is any.

many thanks,

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:

To search Galaxy mailing lists use the unified search at: