Question: build-in custom genomes
gravatar for n.goue
13 months ago by
n.goue50 wrote:


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?

Many thanks!

rna-seq galaxy • 550 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by n.goue50
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I do not see an obvious issue with the data config. That said, you probably still need to update these master locs: dbkeys.loc, alignseq.loc, all_fasta.loc. Often tools depend on samtools being indexed for the genome (and a symlink to the samtools index placed with the mapper indexes, plus the samtools loc updated). Be careful to not duplicate any dbkeys (database short name, e.g. hg19).

Data managers are the best way to install local data. Since you are already using 17.05, you might want to wait a few days and upgrade to the upcoming release 17.09. This might resolve the DM issues.

There are some known issues with Data managers, and these are being rewritten to use the new dependency methods (conda). One issue we found is that the core tool (example: BWA) needs to be installed before the BWA Data manager is used - although that does not sound like your issue.

This help for installing manual genomes is a bit older, and therefore use older tool versions as examples, but the core methods are still good models. Methods to download and use the indexes/locs available at from the rsync server are also covered.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson25k
gravatar for n.goue
13 months ago by
n.goue50 wrote:

Dear Jen,

Thank you for your reply. I updated the dbkeys.loc, didn't modified the alignseq.loc (as I don't use it) and all_fasta.loc file looks good. The restart didn't change anything. Finally, I came back to the data manager and solved the problem by installing the package : data_manager_fetch_genome_dbkeys_all_fasta

However, I was hoping to find a solution to include indexes by hand as I already have the indexes on the server and not to re-run them all through galaxy data manager.

Thank you for your time,

ADD COMMENTlink written 13 months ago by n.goue50

You could check the difference between the files on the system before and after running the Data manager to see what other changes are needed. That is probably the most direct way of finding out extra data is needed when creating indexes without a data manager.

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson25k


I did a git diff on my folders, but nothing special pop-up.


ADD REPLYlink written 13 months ago by n.goue50
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