Hello all,
I have been trying to fix the index problem of BFast since last week, somehow,
the index didn't show in the drop-down box no matter how I managed to modify
the configurations. I listed my steps in the following, hopefully you can help
me to point out where the problem is:
Taken one example for Ecoli.
The index files plus a symbolic link of the genome file for Bfast are stored in
==> /galaxyIndices/genomes/Ecoli/eschColi_K12/bfast
I check the global conf files, tool_conf.xml and tool_data_table_conf.xml,
which both contain the relevant files (sr_mapping/bfast_wrapper.xml and
tool-data/bfast_indexes.loc) for bfast.
The index should be displayed through the following codes in
tools/sr_mapping/bfast_wrapper.xml:
<when value="indexed">
<param name="indices" type="select" label="Select a reference genome">
<options from_data_table="bfast_indexes">
<filter type="multiple_splitter" column="2" separator=","/>
<filter type="param_value" column="2" ref="input1"
ref_attribute="extension"/>
<filter type="sort_by" column="3"/>
<validator type="no_options" message="No indexes are available for
the selected input dataset"/>
</options>
</param>
</when>
And the bfast_indexes ==> "tool-data/bfast_indexes.loc", which points to the
directories where the index files are:
#<unique_id> <build> <galaxy format extensions valid1,valid2>
<description> <bfast_index_directory>
eschColi_K12 eschColi_K12 fastqsanger,fastqcssanger eschColi_K12
/galaxyIndices/genomes/Ecoli/eschColi_K12/bfast/eschColi_K12.fa
Any suggestions?
Look forward to your reply.
Best regards,
Sean
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
