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