comparison tool-data/bowtie2_indices.loc.sample @ 1:85e400e1f2dd draft default tip

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author greg
date Thu, 23 Nov 2023 18:36:23 +0000 (13 months ago)
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0:e589aadb5a80 1:85e400e1f2dd
1 <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
2 <tables>
3 <!-- Locations of indexes in the Bowtie2 mapper format -->
4 <table name="bowtie2_indexes" comment_char="#">
5 <columns>value, dbkey, name, path</columns>
6 <file path="tool-data/bowtie2_indices.loc" />
7 </table>
8 </tables>
9 (base) o1-3s4vnf2:bowtie2 gvk$ cd ttol-da
10 -bash: cd: ttol-da: No such file or directory
11 (base) o1-3s4vnf2:bowtie2 gvk$ cd tool-data/
12 (base) o1-3s4vnf2:tool-data gvk$ ll
13 total 8
14 drwxr-xr-x 3 gvk staff 96 Jan 31 2018 .
15 drwxr-xr-x 8 gvk staff 256 Nov 23 13:26 ..
16 -rw-r--r-- 1 gvk staff 1713 Jan 31 2018 bowtie2_indices.loc.sample
17 (base) o1-3s4vnf2:tool-data gvk$ cat bowtie2_indices.loc.sample
18 # bowtie2_indices.loc.sample
19 # This is a *.loc.sample file distributed with Galaxy that enables tools
20 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
21 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
22 # First create these data files and save them in your own data directory structure.
23 # Then, create a bowtie_indices.loc file to use those indexes with tools.
24 # Copy this file, save it with the same name (minus the .sample),
25 # follow the format examples, and store the result in this directory.
26 # The file should include an one line entry for each index set.
27 # The path points to the "basename" for the set, not a specific file.
28 # It has four text columns seperated by TABS.
29 #
30 # <unique_build_id> <dbkey> <display_name> <file_base_path>
31 #
32 # So, for example, if you had hg18 indexes stored in:
33 #
34 # /depot/data2/galaxy/hg19/bowtie2/
35 #
36 # containing hg19 genome and hg19.*.bt2 files, such as:
37 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
38 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
39 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
40 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
41 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
42 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
43 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
44 #
45 # then the bowtie2_indices.loc entry could look like this:
46 #
47 #hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
48 #
49 #More examples:
50 #
51 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
52 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
53 #
54 #