diff tools/mira4/README.rst @ 0:6a88b42ce6b9 draft

Uploaded v0.0.4, previously only on the TestToolShed

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+Galaxy wrapper for the MIRA assembly program (v4.0)
+===================================================
+
+This tool is copyright 2011-2014 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 
+
+It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
+
+A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
+
+Automated Installation
+======================
+
+This should be straightforward. Via the Tool Shed, Galaxy should automatically
+install the 'mira' datatype, samtools, and download and install the precompiled
+binary for MIRA v4.0.2 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: 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 four Galaxy files to install:
+
+* ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage)
+* ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
+* ``mira4_convert.xml`` (the Galaxy tool definition for converting MIRA files)
+* ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
+* ``mira4.py`` (the Python wrapper script)
+* ``mira4_convert.py`` (the Python wrapper script for miraconvert)
+* ``mira4_bait.py`` (the Python wrapper script for mirabait)
+* ``mira4_validator.py`` (the XML parameter validation script)
+
+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 the tests::
+
+  <tool file="mira4/mira4_de_novo.xml" />
+  <tool file="mira4/mira4_mapping.xml" />
+
+You will also need to install MIRA, we used version 4.0.2, and define the
+environment variable ``$MIRA4`` pointing at the folder containing the binaries.
+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.
+
+You will also need to install samtools (for generating a BAM file from MIRA's
+SAM output).
+
+After copying (or symlinking) the ``test-data`` files under Galaxy's ``test-data``
+folder, you can run the tests with::
+
+    $ ./run_functional_tests.sh -id mira_4_0_bait
+    $ ./run_functional_tests.sh -id mira_4_0_de_novo
+    $ ./run_functional_tests.sh -id mira_4_0_mapping
+    $ ./run_functional_tests.sh -id mira_4_0_convert
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
+v0.0.2  - Include BAM output (using ``miraconvert`` and ``samtools``).
+        - Updated to target MIRA 4.0.1
+        - Simplified XML to apply input format to output data.
+        - Sets temporary folder at run time to respect environment variables
+          (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
+          previously hard coded as ``/tmp``.
+v0.0.3  - Updated to target MIRA 4.0.2
+v0.0.4  - Using optparse for the Python wrapper script API
+        - Made MAF and BAM outputs optional
+        - Include wrapper for ``miraconvert``
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
+
+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_bait.xml tools/mira4/mira4_convert.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_convert.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/header.mira test-data/empty_file.dat
+
+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_bait.xml
+    tools/mira4/mira4_convert.xml
+    tools/mira4/mira4.py
+    tools/mira4/mira4_make_bam.py
+    tools/mira4/mira4_validator.py
+    tools/mira4/mira4_convert.py
+    tools/mira4/mira4_bait.py
+    tools/mira4/tool_dependencies.xml
+    tools/mira4/repository_dependencies.xml
+    test-data/U13small_m.fastq
+    test-data/U13small_m.mira4_de_novo.fasta
+    test-data/tvc_mini.fastq
+    test-data/tvc_contigs.fasta
+    test-data/tvc_map_ref_strain.fasta
+    test-data/tvc_map_same_strain.fasta
+    test-data/tvc_bait.fasta
+    test-data/tvc_mini_bait_pos.fastq
+    test-data/tvc_mini_bait_strict.fastq
+    test-data/tvc_mini_bait_neg.fastq
+    test-data/ecoli.fastq
+    test-data/ecoli.mira4_de_novo.fasta
+    test-data/header.mira
+    test-data/empty_file.dat
+
+
+
+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.