Local Galaxy: Need help with HISAT index builder

Question

[thefirstrealace]

Hello everybody,

i recently installed a local galaxy version and added some tools via toolshed including HISAT. I attempted to build an index for hg19 with the HISAT index builder, but it wont work at all. This is what i have done so far:

1. Install HISAT (+ all dependencies automatically)
2. Install HISAT index builder, which is now available under Data Manager Tools in the Admin section
3. I uploaded the hg19.fa into my galaxy library and imported it into my history

Now when starting the index builder, it wont let me choose my hg19 fasta file. I tried to fight my way through the local galaxy documentation, but it was rather confusing for me. I found out about the rsync, which lets you download genomes/indexes for the commonly used tools (e.g. TopHat, BWA, Bowtie ...), but unfortunately, no HISAT indexes can be downloaded.

So basically, i have to go back to my initial attempt. I really need to build an index with the installed index builder in my local galaxy. What did i do wrong until this point? I hope somebody can help me with this issue.

Best regards and as always thank you in advance for any help and suggestions.

Answer 1

[Devon Ryan]

I actually link our indices in. For example, our computer cluster has HISAT indices in /data/repository/organisms/GRCh38_ensembl/HISATIndex. Since that path is available to Galaxy as well, I just modify the .loc file under tool-data to add that path. Then I don't need to bother with a separate index for Galaxy.

Regarding the hisat data manager, it doesn't accept items in the history (I'm sure there was a reason for that, but I don't know what it is). It will only index genomes listed in the all_fasta.loc file in tool-data/ (that's what these lines in the xml file mean). So you'll need to find that file associated with your dataset in Galaxy and then add it to all_fasta.loc. Then restart Galaxy and then data manager should pick things up.

As an aside, you might want to post Galaxy questions on the Galaxy site. There aren't all that many of us here with Galaxy admin/usage experience.

[thefirstrealace]

Hi,

your method worked perfectly fine. I could directly use the downloaded ht2 indexes from the hisat homepage after changing the .loc file and restarting my local galaxy. Thanks alot for the help.