comparison README @ 7:a18e157ce6e6 draft

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SoftSearch Integrate through galaxy tool shed Guide

1. set tool dependency dir path by removing comment from,
    #tool_dependency_dir = path/to/directory/ from universe_wsgi.ini file 

2. select galaxy main tool shed and type "softsearch_dependency" and install it.(it install binaries of softsearch).

## select fasta file from database instead of history.

Select fasta_indexes.loc file from local catch(from database).
go to /galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/plus91-technologies-pvt-ltd/softsearch/e3609c8714fb/

open the fasta_indexes.loc file and make changes like

        <unique_build_id>	<dbkey>	<display_name>	<file_base_path>

        eg: hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa

open shed_tool_data_table_conf.xml file and add following.

   	<tables>
	    <table name="fasta_indexes" comment_char="#">
      	    <columns>value, dbkey, name, path</columns>
       	    <file path="/path/to/fasta_indexes.loc" />
  	    </table>
	</tables>




Notes:
- It is a dependent tool it require samtools(version above 0.1.18)