Mercurial > repos > peterjc > mira4_assembler
diff tools/mira4_0/README.rst @ 2:4eb32a3d67d1 draft
v0.0.8 - renamed folder, added note about mirabait
author | peterjc |
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date | Wed, 02 Sep 2015 07:46:29 -0400 |
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children | a4f602cc3aa9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira4_0/README.rst Wed Sep 02 07:46:29 2015 -0400 @@ -0,0 +1,157 @@ +Galaxy wrapper for the MIRA assembly program (v4.0) +=================================================== + +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 (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 various Python and XML files to install into Galaxy: + +* ``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_0`` folder. You will also need to +modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool:: + + <tool file="mira4_0/mira4_de_novo.xml" /> + <tool file="mira4_0/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). + +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 mira_4_0_bait + $ ./run_tests.sh -id mira_4_0_de_novo + $ ./run_tests.sh -id mira_4_0_mapping + $ ./run_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`` +v0.0.5 - Tool definition now embeds citation information. +v0.0.6 - Fixed error handling in ``mira4_convert.py``. +v0.0.7 - Renamed folder (internal change only). + - Reorder XML elements (internal change only). + - Use the ``format_source=...`` tag in the MIRA bait wrapper. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package. +v0.0.8 - Renamed folder now have a MIRA 4.9.x wrapper (internal change only). +======= ====================================================================== + + +Developers +========== + +Development is on a dedicated GitHub repository: +https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0 + +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/mira4_0/ + ... + +or:: + + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_0/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira4_0/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/U13small_m.fastq + ... + + +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.