Question: (Closed) Adding a reference genome to a local Galaxy
gravatar for gkuffel22
7 months ago by
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:

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.


  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 7 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.


ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.
The thread is closed. No new answers may be added.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour