Question: How to configure genome in "Map with BWA" (existing tool) after adding it to my local section
gravatar for 18Kbeyond
14 months ago by
New York
18Kbeyond20 wrote:

Hi. I have added the lines below to the section I made in config/tool_conf.xml file and "Map with BWA" is showing up on galaxy interface when I execute However, I can't pick a genome in the "Using reference genome" box.

What modification should I make in shed_tools/ (or is there something else I need to do ) so as to add reference genome path? Thank you.

<tool file="../shed_tools/" guid="">
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson25k • written 14 months ago by 18Kbeyond20
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Did you load any genomes and create indexes yet?

If not, install Data Managers from the Tool Shed and run them from the Admin area (local data). The usual order is:

  • Fetch the genome and create a dbkey
  • Samtools index
  • Picard index
  • TwoBit index
  • Followed by other tool indexes, including BWA

BWA for Illumina has been deprecated - upgrading to BWA/BWA-MEM for both the mapping tool and the Data Manager indexes is strongly recommended. Indexes for any tool are usually tool and tool version specific. Some exceptions are those that make use of the twoBit index (a few different tools use these same data).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson25k

Thank you. Instead of installing data manager from the tool shed, I made my own genome and index and make changes in tool-data/bwa_mem_index.loc

hg19bwa hg19 hg19 Canonical /home/galaxy/galaxy_data/genomes/hg19/bwa/hg19.fa

mm10bwa mm10 mm10 Canonical /home/galaxy/galaxy_data/genomes/mm10/bwa/mm10.fa

ADD REPLYlink modified 14 months ago • written 14 months ago by 18Kbeyond20

However, when I execute the job, it generates the following error:

Traceback (most recent call last):

File "/data/galaxy/lib/galaxy/jobs/runners/", line 130, in queue_job

job_wrapper.finish( stdout, stderr, exit_code )

File "/data/galaxy/lib/galaxy/jobs/", line 1266, in finish

dataset.datatype.set_meta( dataset, overwrite=False )

File "/data/galaxy/lib/galaxy/datatypes/", line 394, in set_meta

exit_code = args=command, stderr=open( stderr_name, 'wb' ) )

File "/usr/local/lib/python2.7/", line 522, in call

return Popen(popenargs, *kwargs).wait()

File "/usr/local/lib/python2.7/", line 710, in __init__ errread, errwrite)

File "/usr/local/lib/python2.7/", line 1335, in _execute_child raise child_exception

OSError: [Errno 2] No such file or directory

ADD REPLYlink modified 14 months ago • written 14 months ago by 18Kbeyond20
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