Mercurial > repos > plus91-technologies > softsearch
comparison README @ 7:a18e157ce6e6 draft
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| author | plus91-technologies |
|---|---|
| date | Fri, 06 Jun 2014 10:06:08 -0400 |
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| 6:c82ca5cd3c3a | 7:a18e157ce6e6 |
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| 1 SoftSearch Integrate through galaxy tool shed Guide | |
| 2 | |
| 3 1. set tool dependency dir path by removing comment from, | |
| 4 #tool_dependency_dir = path/to/directory/ from universe_wsgi.ini file | |
| 5 | |
| 6 2. select galaxy main tool shed and type "softsearch_dependency" and install it.(it install binaries of softsearch). | |
| 7 | |
| 8 ## select fasta file from database instead of history. | |
| 9 | |
| 10 Select fasta_indexes.loc file from local catch(from database). | |
| 11 go to /galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/plus91-technologies-pvt-ltd/softsearch/e3609c8714fb/ | |
| 12 | |
| 13 open the fasta_indexes.loc file and make changes like | |
| 14 | |
| 15 <unique_build_id> <dbkey> <display_name> <file_base_path> | |
| 16 | |
| 17 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa | |
| 18 | |
| 19 open shed_tool_data_table_conf.xml file and add following. | |
| 20 | |
| 21 <tables> | |
| 22 <table name="fasta_indexes" comment_char="#"> | |
| 23 <columns>value, dbkey, name, path</columns> | |
| 24 <file path="/path/to/fasta_indexes.loc" /> | |
| 25 </table> | |
| 26 </tables> | |
| 27 | |
| 28 | |
| 29 | |
| 30 | |
| 31 Notes: | |
| 32 - It is a dependent tool it require samtools(version above 0.1.18) |