Mercurial > repos > fubar > weblogo3

annotate rgweblogo/README @ 7:6027af2c1af8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Wed, 25 Sep 2013 21:19:44 -0400
parents 78fe723fde78
children 01ec43556e16
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
1 This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
2
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
3 It generates sequence logos from fasta files such as the alignments generated by clustalw
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
4
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
5 Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
6
3
78fe723fde78 Uploaded
fubar
parents: 0
diff changeset
7 **Automated Installation**
78fe723fde78 Uploaded
fubar
parents: 0
diff changeset
8 As a Galaxy admin, use the admin menu and select the search ToolShed option. This tool should be on the main toolshed - if not try the test toolshed.
78fe723fde78 Uploaded
fubar
parents: 0
diff changeset
9 Select it and choose "preview and install" - the process of downloading and installing weblogo3.3 and this wrapper should take a few minutes at most.
78fe723fde78 Uploaded
fubar
parents: 0
diff changeset
10
78fe723fde78 Uploaded
fubar
parents: 0
diff changeset
11 ** Manual Installation**
0
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
12
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
13 Make sure weblogo3 is installed in your system python and is available on the path for all your nodes
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
14
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
15 Move the test data files to your galaxy root test-data
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
16 Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there.
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
17 Run
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
18 sh run_functional_tests.sh -id weblogo3
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
19 to make sure the tests work
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
20
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
21 then restart Galaxy and you should be good to go.
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
22
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
23
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
24 **Attribution**
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
25
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
26 Source for the weblogo3 python executable is at http://weblogo.berkeley.edu
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
27
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
28 Written by Ross Lazarus for the Rgenetics project
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
29
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
30 Copyright Ross Lazarus at gmail com 2011
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
31
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
32 All rights reserved.
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
33
ea6678917716 Migrated tool version 0.1 from old tool shed archive to new tool shed repository
fubar
parents:
diff changeset
34 Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html