Mercurial > repos > plus91-technologies > softsearch
changeset 7:a18e157ce6e6 draft
Uploaded
| author | plus91-technologies |
|---|---|
| date | Fri, 06 Jun 2014 10:06:08 -0400 |
| parents | c82ca5cd3c3a |
| children | 6a5d5546adce |
| files | README |
| diffstat | 1 files changed, 32 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Jun 06 10:06:08 2014 -0400 @@ -0,0 +1,32 @@ +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)