Mercurial > repos > nilshomer > tmap_wrapper

annotate tmap_wrapper_0.3.3/tmap_index.loc.sample @ 2:e2640d81157a default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
* moving to TMAP 0.3.3
author Nils Homer <nilshomer@gmail.com>
date Sun, 26 Feb 2012 20:28:27 -0500
parents tmap_wrapper_0.0.19/tmap_index.loc.sample@de2efe4dda3f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
2 #to use a directory of TMAP indexed sequences data files. You will need
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
3 #to create these data files and then create a tmap_index.loc file
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
5 #the directories in which those files are stored. The tmap_index.loc
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
6 #file has this format (longer white space characters are TAB characters):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
7 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
8 #<unique_build_id> <dbkey> <display_name> <file_path>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
9 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
10 #So, for example, if you had phiX indexed stored in
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
11 #/depot/data2/galaxy/phiX/base/,
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
12 #then the tmap_index.loc entry would look like this:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
13 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
15 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
16 #and your /depot/data2/galaxy/phiX/base/ directory
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
17 #would contain phiX.fa.* files:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
18 #
2
e2640d81157a * moving to TMAP 0.3.3
Nils Homer <nilshomer@gmail.com>
parents: 0
diff changeset
19 #-rw-r--r-- 1 nhomer staff 5.3K Feb 25 21:19 phi.x.174.fa
e2640d81157a * moving to TMAP 0.3.3
Nils Homer <nilshomer@gmail.com>
parents: 0
diff changeset
20 #-rw-r--r-- 1 nhomer staff 24B Feb 24 14:50 phi.x.174.fa.fai
e2640d81157a * moving to TMAP 0.3.3
Nils Homer <nilshomer@gmail.com>
parents: 0
diff changeset
21 #-rw-r--r-- 1 nhomer staff 68B Feb 25 21:19 phi.x.174.fa.tmap.anno
e2640d81157a * moving to TMAP 0.3.3
Nils Homer <nilshomer@gmail.com>
parents: 0
diff changeset
22 #-rw-r--r-- 1 nhomer staff 1.3M Feb 25 21:19 phi.x.174.fa.tmap.bwt
e2640d81157a * moving to TMAP 0.3.3
Nils Homer <nilshomer@gmail.com>
parents: 0
diff changeset
23 #-rw-r--r-- 1 nhomer staff 1.3K Feb 25 21:19 phi.x.174.fa.tmap.pac
e2640d81157a * moving to TMAP 0.3.3
Nils Homer <nilshomer@gmail.com>
parents: 0
diff changeset
24 #-rw-r--r-- 1 nhomer staff 2.6K Feb 25 21:19 phi.x.174.fa.tmap.sa
0
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
25 #...etc...
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
26 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
27 #Your tmap_index.loc file should include an entry per line for each
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
28 #index set you have stored. The "file" in the path does not actually
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
29 #exist, but it is the prefix for the actual index files. For example:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
30 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
31 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
32 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
33 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
34 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
35 #...etc...
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
36 #
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
37 #Note that for backwards compatibility with workflows, the unique ID of
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
38 #an entry must be the path that was in the original loc file, because that
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
39 #is the value stored in the workflow for that parameter. That is why the
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
40 #hg19 entry above looks odd. New genomes can be better-looking.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
nilshomer
parents:
diff changeset
41 #