Hello,
we're in the process of installing bowtie and bwa to get them working with Galaxy and have a question. Looking at left hand menu item "NGS: Mapping" on the home page of Galaxy that we have just installed we see:
NGS: Mapping Megablast compare short reads against nt and wgs databases Parse blast XML output
Digging in tools_config.xml we see:
<section name="NGS: Mapping" id="solexa_tools"> <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> --> <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="sr_mapping/bowtie_wrapper.xml" /> <tool file="sr_mapping/bwa_wrapper.xml" /> </section>
Looking in .../tools/sr_mapping we see both:
bowtie_wrapper.xml bwa_wrapper.xml
And checking say bowtie_wrapper.xml we see
<tool id="bowtie_wrapper" name="Bowtie" version="1.0.0"> <description> fast alignment of reads against reference sequence </ description
Everything looks good so why do we not see sub-menu items for bowtie and bwa? All we see under NGS: Mapping are the two items I listed initially, "Megablast compare short reads against nt and wgs databases" and "Parse blast XML output".
Thanks for your help. Mark.