How to build a "build in" bowtie index in galaxy?

Question

[yangmqglobe]

I was using a local galaxy and that I found it wasn't easy to add a "build in" bowtie index. First, I've install the data_manager_bowtie_index_builder via toolsheld, and then upload the hg19.fa(download the hg19.2bit from UCSC and cover to fasta format) to the history. But I found the tool wouldn't let me to select this file as an input, I've found some kind of the same question like this:Local Galaxy: Need help with HISAT index builder, but there wasn't a clear solution, and I've check the document like this:https://galaxyproject.org/admin/data-preparation/ and I don't seen it is work for me, so what is the way to add a "build in" bowtie index?

Answer 1

[Devon Ryan]

You should post on the galaxy biostar instead.

Anyway, as I replied in the post you linked to, your fasta file needs to be in the all_fasta data table. You'll need to edit that file and reload it.

[yangmqglobe]

First of all, thank you for your help. But I am still confuse, cause it never work for me? So I download the hg19 genome and add one line in the galaxy/tool-data/all-fasta.loc like this:

hg19(\t)hg19(\t)Hunman Feb. 2009 (GRCh39/19)(hg19)(\t)/path/to/download/hg19.fa

After I restart the galaxy, he still wouldn't let me select the genome fasta file

[Devon Ryan]

Does that line show up when you look at the data table in Galaxy ("Admin" -> "Local data")? Also all_fasta.loc, not all-fasta.loc.

[yangmqglobe]

Yes, it is all_fasta.loc, I make a mistake