Question: (Closed) Adding a reference genome to a local Galaxy
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gravatar for gkuffel22
5 months ago by
gkuffel22170
United States
gkuffel22170 wrote:

Hoping to find some Galaxy Dev team experts. I am trying to add hg38 to the HiSat2 tool so that the genome is built in. I have followed the tutorial located at: https://galaxyproject.org/admin/data-integration/

Here are the steps I followed:

  1. I used HiSat2 through the command line to create the hisat2 indexes.

  2. I created a directory in the following location to contain the hg38 genome and newly created indexes.

    /home/galaxy/data/galaxy/tool-data/genome/GRCh38/hisat2_indexes

  3. I modified the hisat2.loc file to list hg38 as shown below:

    GRCh38 GRCh38 Human_Aug._2015_(GRCh38) /home/galaxy/data/galaxy/tool-data/genome/GRCh38/hisat2_indexes/GRCh38

(I created above using nano on the command line. Maybe it's not tab-delimited? I intended it to be.)

  1. I double checked to see if the hisat.xml file contained the correct referece to the data table:

    <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="hisat2_indexes">

  2. I restarted the server and to my dismay there is no hg38 genome in the drop down menu for hisat2.

Can anyone help? What am I missing? Thanks.

ADD COMMENTlink written 5 months ago by gkuffel22170

Hello gkuffel22!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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