Mercurial > repos > peterjc > venn_list
comparison tools/plotting/venn_list.rst @ 6:6ebfb498c2c4 draft
Uploaded v0.0.6 take 3, MIT licence, RST README, citation information
| author | peterjc |
|---|---|
| date | Wed, 11 Sep 2013 06:46:31 -0400 |
| parents | |
| children | 978617e4b6a4 |
comparison
equal
deleted
inserted
replaced
| 5:51fe47a5a803 | 6:6ebfb498c2c4 |
|---|---|
| 1 Galaxy tool to draw a Venn Diagram with up to 3 sets | |
| 2 ==================================================== | |
| 3 | |
| 4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute | |
| 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
| 6 See the licence text below. | |
| 7 | |
| 8 This tool is a short Python script (using both the Galaxy and Biopython library | |
| 9 functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build | |
| 10 sets, which are then drawn using the R limma package function vennDiagram | |
| 11 (called from Python using rpy). | |
| 12 | |
| 13 There are just two files to install: | |
| 14 | |
| 15 * venn_list.py (the Python script) | |
| 16 * venn_list.xml (the Galaxy tool definition) | |
| 17 | |
| 18 The suggested location is in the Galaxy folder tools/plotting next to other | |
| 19 graph drawing tools. | |
| 20 | |
| 21 You will also need to install Biopython 1.54 or later, and the R/Bioconductor | |
| 22 pacakge limma. You should already have rpy installed for other Galaxy tools. | |
| 23 | |
| 24 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
| 25 tool. The suggested location is in the "Graph/Display Data" section. Simply add | |
| 26 the line:: | |
| 27 | |
| 28 <tool file="plotting/venn_list.xml" /> | |
| 29 | |
| 30 If you wish to run the unit tests, also add this to tools_conf.xml.sample and | |
| 31 move/copy the test-data files under Galaxy's test-data folder. Then:: | |
| 32 | |
| 33 ./run_functional_tests.sh -id venn_list | |
| 34 | |
| 35 | |
| 36 History | |
| 37 ======= | |
| 38 | |
| 39 ======= ====================================================================== | |
| 40 Version Changes | |
| 41 ------- ---------------------------------------------------------------------- | |
| 42 v0.0.3 - Initial public release. | |
| 43 v0.0.4 - Ignore blank lines when loading IDs from tabular files | |
| 44 v0.0.5 - Explicit Galaxy error handling of return codes | |
| 45 v0.0.6 - Added unit tests. | |
| 46 - Use reStructuredText for this README file. | |
| 47 - Adopt standard MIT licence. | |
| 48 - Updated citation information (Cock et al. 2013). | |
| 49 ======= ====================================================================== | |
| 50 | |
| 51 | |
| 52 Developers | |
| 53 ========== | |
| 54 | |
| 55 This script and related tools are being developed on the following hg branch: | |
| 56 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 57 | |
| 58 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
| 59 the following command from the Galaxy root folder:: | |
| 60 | |
| 61 $ tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta | |
| 62 | |
| 63 Check this worked:: | |
| 64 | |
| 65 $ tar -tzf venn_list.tar.gz | |
| 66 tools/plotting/venn_list.py | |
| 67 tools/plotting/venn_list.rst | |
| 68 tools/plotting/venn_list.xml | |
| 69 test-data/venn_list1.pdf | |
| 70 test-data/venn_list.tabular | |
| 71 test-data/rhodopsin_proteins.fasta | |
| 72 | |
| 73 | |
| 74 Licence (MIT) | |
| 75 ============= | |
| 76 | |
| 77 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 78 of this software and associated documentation files (the "Software"), to deal | |
| 79 in the Software without restriction, including without limitation the rights | |
| 80 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 81 copies of the Software, and to permit persons to whom the Software is | |
| 82 furnished to do so, subject to the following conditions: | |
| 83 | |
| 84 The above copyright notice and this permission notice shall be included in | |
| 85 all copies or substantial portions of the Software. | |
| 86 | |
| 87 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 88 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 89 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 90 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 91 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 92 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 93 THE SOFTWARE. |