Mercurial > repos > peterjc > venn_list
view tools/venn_list/README.rst @ 23:c4ec51cb5acc draft
Tool Shed dependency for rpy and limma; update README
author | peterjc |
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date | Sat, 10 Oct 2015 08:51:00 -0400 |
parents | 2a1025bbd637 |
children | 2f2c62ec2d08 |
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Galaxy tool to draw a Venn Diagram with up to 3 sets ==================================================== This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This tool is a short Python script (using both the Galaxy and Biopython library functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build sets, which are then drawn using the R limma package function vennDiagram (called from Python using rpy). This tool is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list Automated Installation ====================== This should be straightforward, Galaxy should automatically download the tool and the Python dependencies Biopython and rpy, and the R/Bioconductor package limma. Manual Installation =================== There are just two files to install: * ``venn_list.py`` (the Python script) * ``venn_list.xml`` (the Galaxy tool definition) The suggested location is in the Galaxy folder ``tools/plotting`` next to other graph drawing tools, or a dedicated ``tools/venn_list`` directory. You will also need to install Biopython 1.54 or later, and the R/Bioconductor package limma. You should already have rpy installed for other Galaxy tools. You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool. The suggested location is in the "Graph/Display Data" section. Simply add the line:: <tool file="venn_list/venn_list.xml" /> If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: ./run_tests.sh -id venn_list History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.3 - Initial public release. v0.0.4 - Ignore blank lines when loading IDs from tabular files v0.0.5 - Explicit Galaxy error handling of return codes v0.0.6 - Added unit tests. - Use reStructuredText for this README file. - Adopt standard MIT licence. - Updated citation information (Cock et al. 2013). - Development moved to GitHub, https://github.com/peterjc/pico_galaxy v0.0.7 - Renamed folder and README file. - Tool definition now embeds citation information. v0.0.8 - Reorder XML elements (internal change only). - Fixed and improved error handling when rpy is not available. - Test output relaxed to cope with more variation in PDF output. - Declare Biopython dependency via the Tool Shed. v0.0.9 - Test with three-way Venn diagram. - Includes testing of failure mode. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Tool Shed dependency for rpy and limma (thanks to Björn Grüning). ======= ====================================================================== Developers ========== This script and related tools were initially developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ ... or:: $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ ... $ tar -tzf shed_upload.tar.gz tools/venn_list/README.rst tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.py tools/venn_list/venn_list.xml test-data/magic.pdf test-data/rhodopsin_proteins.fasta test-data/venn_list.tabular Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.