Mercurial > repos > plus91-technologies > softsearch
comparison README @ 24:8578d978014c draft
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| author | plus91-technologies |
|---|---|
| date | Mon, 09 Jun 2014 06:02:39 -0400 |
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| 23:3837fa11246b | 24:8578d978014c |
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| 1 SoftSearch Integrate through galaxy tool shed Guide | |
| 2 | |
| 3 1. What to do for SoftSearch. | |
| 4 | |
| 5 must login as a admin, for that you may change the universe_wsgi.ini file like remove comment. | |
| 6 #admin_users = name@sample.com | |
| 7 | |
| 8 | |
| 9 2. How to install. | |
| 10 | |
| 11 Go to Admin at top of galaxy and select "Search and browse tool sheds" from tool sheds, select "galaxy main | |
| 12 tool shed" and type "softsearch" and install.(It download all binaries). | |
| 13 | |
| 14 | |
| 15 3. Select fasta file from database. | |
| 16 | |
| 17 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/ | |
| 18 3837fa11246b/softsearch/tool-data/ | |
| 19 | |
| 20 --open the fasta_indexes.loc file and make changes like | |
| 21 | |
| 22 <unique_build_id> <dbkey> <display_name> <file_base_path> | |
| 23 | |
| 24 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa | |
| 25 | |
| 26 --open shed_tool_data_table_conf.xml file and add following. | |
| 27 | |
| 28 <tables> | |
| 29 <table name="fasta_indexes" comment_char="#"> | |
| 30 <columns>value, dbkey, name, path</columns> | |
| 31 <file path="/path/to/fasta_indexes.loc" /> | |
| 32 </table> | |
| 33 </tables> | |
| 34 | |
| 35 | |
| 36 | |
| 37 Notes: | |
| 38 | |
| 39 - It is a dependent tool it may require samtools(version above 0.1.18) |