Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite/README @ 0:e590e0f70b60 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 15:59:36 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
1 -----------------------------------------------------------------------
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
2 CADDSuite - A flexible and open framework and workflow system
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
3 for computer-aided drug design
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
4 -----------------------------------------------------------------------
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
5
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
6 This package contains all tools belonging to CADDSuite.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
7 For an overview over the contained tools, please see CADDSuite-description.txt.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
8 After extraction the package, you can directly start the applications using the startup-scripts in the base-folder.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
9
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
10 For more information about an individual tool, please call the tool without any parameters (or with '-h').
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
11
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
12
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
13
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
14 --------------------------------------------------------------------
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
15 Instructions for integration of CADDSuite into the workflow-system
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
16 Galaxy (http://getgalaxy.org)
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
17 --------------------------------------------------------------------
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
18
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
19
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
20 In order to install CADDSuite into your Galaxy installation, please to the following:
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
21
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
22 Let's assume $galaxybase is the base-folder of your Galaxy installation.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
23 If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
24
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
25
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
26 -- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
27
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
28 After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below:
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
29
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
30 -- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
31
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
32 -- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
33
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
34 -- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
35
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
36
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
37
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
38 Last but not least, restart Galaxy.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
39 All CADDSuite tools should now appear in your Galaxy webinterface.
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
40
e590e0f70b60 Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
41