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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 installation.
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4
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5 ---set tool dependency dir path by removing comment from,
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6 #tool_dependency_dir = path/to/directory/ from universe_wsgi.ini file
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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 ---select galaxy main tool shed and type "softsearch_dependency" and install it.(it install binaries of softsearch).
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12
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13
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14 3. Access fasta file from Database instead of history.
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15
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16 ---Select fasta_indexes.loc file from local catch(from database).
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17 go to /galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/plus91-technologies-pvt-ltd/softsearch/e3609c8714fb/
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18
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19 ---open the fasta_indexes.loc file and make changes like
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20
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21 <unique_build_id> <dbkey> <display_name> <file_base_path>
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22
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23 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/hg19full.fa
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24
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25 ---open shed_tool_data_table_conf.xml file and add following.
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26
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27 <tables>
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28 <table name="fasta_indexes" comment_char="#">
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29 <columns>value, dbkey, name, path</columns>
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30 <file path="/path/to/fasta_indexes.loc" />
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31 </table>
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32 </tables>
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33
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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 - It is a dependent tool it require samtools(version above 0.1.18)
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