Mercurial > repos > peterjc > venn_list
diff README.rst @ 15:367a0403b7d2 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/venn_list commit 6c4ac223d511bbcd0ec9cbada730613a5fe9f1af-dirty
author | peterjc |
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date | Thu, 07 May 2015 05:43:50 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu May 07 05:43:50 2015 -0400 @@ -0,0 +1,125 @@ +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 Biopython dependency. + +You will still need to install 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. +======= ====================================================================== + + +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 "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ +use the following Planemo command (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_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ + ... + $ tar -tzf shed_upload.tar.gz + README.rst + test-data/magic.pdf + test-data/rhodopsin_proteins.fasta + test-data/venn_list.tabular + tool_dependencies.xml + venn_list.py + venn_list.xml + +This tar-ball can be uploaded to the Tool Shed via the web interface (using +the ``--tar`` command or via +Planemo. More simply, the following single command can be used: + + $ planemo shed_upload + + +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.