diff tools/mira4/README.rst @ 0:32f693f6e741 draft

Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency

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+Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
+=============================================================
+
+This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This tool is a short Python script (to collect the MIRA output and move it
+to where Galaxy expects the files) and associated Galaxy wrapper XML file.
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler 
+
+
+Automated Installation
+======================
+
+This should be straightforward. Via the Tool Shed, Galaxy should automatically
+install the 'mira' datatype, download and install the precompiled binary for
+MIRA v4.0 for the Galaxy wrapper, and run any tests.
+
+For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
+cluster settings for de novo usage (high RAM) and mapping (lower RAM).
+Consult the Galaxy adminstration documentation for your cluster setup.
+
+WARNING: This tool was developed to construct viral genome assembly and
+mapping pipelines, for which the run time and memory requirements are
+negligible. For larger tasks, be aware that MIRA can require vast amounts
+of RAM and run-times of over a week are possible. This tool wrapper makes
+no attempt to spot and reject such large jobs.
+
+
+Manual Installation
+===================
+
+First install the 'mira' datatype for Galaxy, available here:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes 
+
+There are just two Galaxy files to install:
+
+* mira4.py (the Python script)
+* mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
+* mira4_mapping.xml (the Galaxy tool definition for mapping usage)
+
+The suggested location is a new tools/mira4 folder. You will also need to
+modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
+this to tools_conf.xml.sample in order to run any tests::
+
+  <tool file="mira4/mira4_de_novo.xml" />
+  <tool file="mira4/mira4_mapping.xml" />
+
+You will also need to install MIRA, we used version 4.0 RC2. See:
+
+* http://chevreux.org/projects_mira.html
+* http://sourceforge.net/projects/mira-assembler/
+
+You may wish to use different cluster setups for the de novo and mapping
+tools, see above.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version (prototype using MIRA 4.0 RC2, and wrapper for v3.4)
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs_mira4.fasta
+
+Check this worked::
+
+    $ tar -tzf mira4_wrapper.tar.gz
+    tools/mira4/README.rst
+    tools/mira4/mira4_de_novo.xml
+    tools/mira4/mira4_mapping.xml
+    tools/mira4/mira4.py
+    tools/mira4/tool_dependencies.xml
+    test-data/tvc_mini.fastq
+    test-data/tvc_contigs_mira4.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.