Question: instructions for fetching and install mm10 genome and hisat indexing for local galaxy
0
gravatar for vaughandy
4 months ago by
vaughandy10
vaughandy10 wrote:

Hi all,

Is there a kind soul that could take me through a step-by-step of fetching and indexing the mouse mm10 genome from UCSC (or wherever) on a local galaxy install, with a data manager? I have the indexers installed as well as create db key, rsync, and fetch reference genome. I just can't seem to make this work. I've also tried indexing a locally cached mm10 reference genome with the hisat indexer, but hisat2 can't seem to use it (see error description in my other post).

I totally realize this is a lot to ask, but maybe somebody is particularly kind and would take pity on me?

Thanks!!@!

ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson22k • written 4 months ago by vaughandy10
1
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

Admin help for Data Managers (and local data in general) is in this recent training material from Galaxy Australia Meeting (GAMe 2017). See the slides and example for Data Mangers listed under Monday's afternoon session here:

Overview instructions are also in this prior post: https://biostar.usegalaxy.org/p/12409/#12468

And the original wiki help is here: https://wiki.galaxyproject.org/Admin/Tools/DataManagers

I am concerned that your data tables might have problems now due to running the data managers a few times on the same dbkey or out of order. Duplicated lines/dbkeys in the data tables can cause problems. Cleaning up that content is non-trivial to do. If possible, you might want to start over in a new instance. Then follow the steps in the links above: retrieve the fasta (allow to complete), index for samtools (allow to complete), index for picard (allow to complete), then index for other tools like HISAT2.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k
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