Question about "reference_fasta_filename" for "Map with BWA" (existing tool)

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Question about "reference_fasta_filename" for "Map with BWA" (existing tool)

Qian, Yingzhi

Hi there,

This is my first time writing to the mailing list. Thanks in advance.


(I have added the lines in PS (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 run.sh. ) However, I can't pick a genome in the "Using reference genome" box. The drop-down box doesn't work.


I have loaded genomes and created indexes to my local galaxy. I just don't know where to insert the path in this file - shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml I see it has "reference_fasta_filename" (reference genome) but I am not sure what it is directing to or what to modify to tell where I put the genomes. Or is there something else I need to do?


Regards,

Ying

PS

<tool file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/051eba708f43/bwa/bwa.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2">
    <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>bwa</repository_name>
            <repository_owner>devteam</repository_owner>
            <installed_changeset_revision>051eba708f43</installed_changeset_revision>
            <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2</id>
            <version>0.7.15.2</version>
</tool>


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