comparison tool-data/smalt_index.loc.sample @ 1:54855bd8d107 draft default tip

First attempt to get tool_dependencies.xml right.
author cjav
date Wed, 20 Mar 2013 17:07:14 -0400
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0:747433a6de00 1:54855bd8d107
1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of Smalt indexed sequences data files. You will need
3 #to create these data files and then create a smalt_index.loc file
4 #similar to this one (store it in this directory) that points to
5 #the directories in which those files are stored. The smalt_index.loc
6 #file has this format (longer white space characters are TAB characters):
7 #
8 #<unique_build_id> <dbkey> <display_name> <file_path>
9 #
10 #So, for example, if you had phiX indexed stored in
11 #/depot/data2/galaxy/phiX/base/,
12 #then the smalt_index.loc entry would look like this:
13 #
14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
15 #
16 #and your /depot/data2/galaxy/phiX/base/ directory
17 #would contain hg19.fa.* files:
18 #
19 #-rw-r--r-- 1 cborroto universe 527388 2005-09-13 10:12 phix.fa.sma
20 #-rw-r--r-- 1 cborroto universe 269808 2005-09-13 10:12 phiX.fa.smi
21 #
22 #Your smalt_index.loc file should include an entry per line for each
23 #index set you have stored. The "file" in the path does not actually
24 #exist, but it is the prefix for the actual index files. For example:
25 #
26 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
27 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
28 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
29