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Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
author nilshomer
date Tue, 07 Jun 2011 17:43:07 -0400
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9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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1 #This is a sample file distributed with Galaxy that enables tools
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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2 #to use a directory of SRMA indexed sequences data files. You will need
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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3 #to create these data files and then create a srma_ref.loc file
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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4 #similar to this one (store it in this directory) that points to
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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5 #the directories in which those files are stored. The srma_ref.loc
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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6 #file has this format (white space characters are TAB characters):
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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7 #
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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8 #<build> <fasta_file>
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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9 #
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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10 #So, for example, if you had hg18 indexed stored in
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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11 #/depot/data2/galaxy/srma/hg18/,
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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12 #then the srma_ref.loc entry would look like this:
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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13 #
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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14 #hg18 /depot/data2/galaxy/srma/hg18/hg18.fa
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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15 #
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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16 #and your /depot/data2/galaxy/srma/hg18/ directory
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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17 #would contain hg18.fa.*.brg and hg18.fa.*.bif files:
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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18 #hg18.fa
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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19 #hg18.fa.dict
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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20 #...etc...
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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21 #
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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22 #The dictionary file for each reference (ex. hg18.fa.dict) must be
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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23 #created with Picard (http://picard.sourceforge.net).
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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24 #
9d60d2fce247 Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
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25 20079 /Users/nhomer/hg/galaxy-central/srma/DH10B.fa