annotate README.rst @ 0:a13b9fcbc0ee

Push to main toolshed
author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 12:44:02 +0100
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
1 PRIMV-visualization toolset & Galaxy wrappers
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
2 =============================================
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
3
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
4 Visualization module of Plant Research International's Multi-purpose Views (PRIMV) toolsuite.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
5
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
6 This toolset consists of tools that generate multi-purpose views to assist in the visualization
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
7 and interpretation of large and complex datasets.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
8
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
9 Can be used a.o. in combination with PRIMS-MASSCOMB (prims_masscomb package) and
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
10 PRIMS-proteomics (prims_proteomics package).
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
11
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
12 Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI),
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
13 Wageningen, The Netherlands. All rights reserved. See the license text below.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
14
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
15 Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
16 http://toolshed.g2.bx.psu.edu/view/pieterlukasse/primv_visualization
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
17
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
18 History
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
19 =======
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
20
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
21 ============== ========================================================================
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
22 Date Changes
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
23 -------------- ------------------------------------------------------------------------
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
24 January 2014 -first release via Tool Shed
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
25 November 2013 -cytoexport tool used internally at PRI
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
26 October 2012 -first tool for generating visually rich Cytoscape networks (cytoexport)
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
27 ============== ========================================================================
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
28
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
29 Tool Versioning
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
30 ===============
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
31
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
32 Tools will have versions of the form X.Y.Z. Versions
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
33 differing only after the second decimal should be completely
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
34 compatible with each other. Breaking changes should result in an
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
35 increment of the number before and/or after the first decimal. All
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
36 tools of version less than 1.0.0 should be considered beta.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
37
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
38
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
39 Bug Reports & other questions
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
40 =============================
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
41
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
42 For the time being issues can be reported via the contact form at
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
43 http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
44
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
45 Developers, Contributions & Collaborations
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
46 ==========================================
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
47
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
48 If you wish to join forces and collaborate on some of the
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
49 tools do not hesitate to contact Pieter Lukasse via the contact form above.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
50
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
51 License (Apache, Version 2.0)
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
52 =============================
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
53
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
54 Copyright 2013 Pieter Lukasse, Plant Research International (PRI).
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
55
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
56 Licensed under the Apache License, Version 2.0 (the "License");
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
57 you may not use this software except in compliance with the License.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
58 You may obtain a copy of the License at
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
59
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
60 http://www.apache.org/licenses/LICENSE-2.0
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
61
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
62 Unless required by applicable law or agreed to in writing, software
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
63 distributed under the License is distributed on an "AS IS" BASIS,
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
64 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
65 See the License for the specific language governing permissions and
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
66 limitations under the License.
a13b9fcbc0ee Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
67