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:
- Install HISAT (+ all dependencies automatically)
- Install HISAT index builder, which is now available under Data Manager Tools in the Admin section
- 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.