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:
I used HiSat2 through the command line to create the hisat2 indexes.
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
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.)
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">
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.
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