instructions for fetching and install mm10 genome and hisat indexing for local galaxy

Question: instructions for fetching and install mm10 genome and hisat indexing for local galaxy

21 months ago by

vaughandy • 10 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!!@!

refererence genome index hisat2 • 786 views

ADD COMMENT • link •

modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by vaughandy • 10

21 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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:

All topics https://github.com/gvlproject/dagobah-training/
- Slides that cover data https://gvlproject.github.io/dagobah-training/05-reference-genomes/reference_genomes.html#1
- Examples for data https://github.com/gvlproject/dagobah-training/blob/master/sessions/05-reference-genomes/ex1-reference-genomes.md

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 COMMENT • link modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »