I am facing problem to make reference genome index available in mapper tools such as BWA, bowtie2 and HiSAT2. Here is what I did:
- upload my genome.fasta file
- build an index
both localized in /data/index/bwa_index, /data/index/bowtie2_index and /data/index/hisat2_index
- I modified the *.loc files
CS1 CS1 Chinese Spring /data/index/bwa_index/CS/wheat_refseq_CS
CS1 CS1 Chinese Spring /data/index/bowtie2_index/CS/wheat_refseq_CS
and tool-data/hisat2_indexes.loc :
CS1 CS1 Chinese Spring /data/index/hisat2_index/CS/wheat_refseq_CS
- I updated the tool-data/shared/ucsc/builds.txt:
CS1 Chinese Spring
- I also checked the config/tool_data_table_conf.xml for my loc.files.
- I over-checked my path (that I cut/paste), also I was careful to add tabulation in all config files.
I am using galaxy v17_05.
On my local computer galaxy instance: only Hisat2 tool give me access to the index in the drop-down "Select a reference genome" menu, while with BWA and Bowtie2, I got a : No options available in the same drop-down menu.
While trying the same steps on our local galaxy instance, none is working.
I tried also to by-pass the problem with the data_manager tool Shed, but also failed to make it worked.
Would you have some ideas what's going wrong?