Mercurial > repos > greg > cfsan_snp_pipeline_map_reads
comparison tool-data/bowtie2_indices.loc.sample @ 1:85e400e1f2dd draft default tip
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author | greg |
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date | Thu, 23 Nov 2023 18:36:23 +0000 (13 months ago) |
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0:e589aadb5a80 | 1:85e400e1f2dd |
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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 # |