diff tools/venn_list/README.rst @ 4:991342eca214 draft

Uploaded v0.0.8a, declare Biopython dependency via Tool Shed

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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 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 making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
+
+Check this worked::
+
+    $ tar -tzf venn_list.tar.gz
+    tools/venn_list/README.rst
+    tools/venn_list/venn_list.py
+    tools/venn_list/venn_list.xml
+    tools/venn_list/tool_dependencies.xml
+    test-data/magic.pdf
+    test-data/venn_list.tabular
+    test-data/rhodopsin_proteins.fasta
+
+
+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.