Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4_0/README.rst @ 4:1713289d9908 draft default tip
v0.0.11 tweak for use with bioconda dependencies
| author | peterjc |
|---|---|
| date | Thu, 10 Aug 2017 11:09:10 -0400 |
| parents | a4f602cc3aa9 |
| children |
| rev | line source |
|---|---|
| 2 | 1 Galaxy wrapper for the MIRA assembly program (v4.0) |
| 2 =================================================== | |
| 3 | |
| 4 | 4 This tool is copyright 2011-2016 by Peter Cock, The James Hutton Institute |
| 2 | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
| 6 See the licence text below (MIT licence). | |
| 7 | |
| 8 This tool is a short Python script (to collect the MIRA output and move it | |
| 9 to where Galaxy expects the files) and associated Galaxy wrapper XML file. | |
| 10 | |
| 11 It is available from the Galaxy Tool Shed at: | |
| 12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler | |
| 13 | |
| 14 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format, | |
| 15 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes | |
| 16 | |
| 17 A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at: | |
| 18 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler | |
| 19 | |
| 20 Automated Installation | |
| 21 ====================== | |
| 22 | |
| 23 This should be straightforward. Via the Tool Shed, Galaxy should automatically | |
| 24 install the 'mira' datatype, samtools, and download and install the precompiled | |
| 25 binary for MIRA v4.0.2 for the Galaxy wrapper, and run any tests. | |
| 26 | |
| 27 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate | |
| 28 cluster settings for de novo usage (high RAM) and mapping (lower RAM). | |
| 29 Consult the Galaxy adminstration documentation for your cluster setup. | |
| 30 | |
| 31 WARNING: For larger tasks, be aware that MIRA can require vast amounts | |
| 32 of RAM and run-times of over a week are possible. This tool wrapper makes | |
| 33 no attempt to spot and reject such large jobs. | |
| 34 | |
| 35 | |
| 36 Manual Installation | |
| 37 =================== | |
| 38 | |
| 39 First install the 'mira' datatype for Galaxy, available here: | |
| 40 | |
| 41 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes | |
| 42 | |
| 43 There are various Python and XML files to install into Galaxy: | |
| 44 | |
| 45 * ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage) | |
| 46 * ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage) | |
| 47 * ``mira4_convert.xml`` (the Galaxy tool definition for converting MIRA files) | |
| 48 * ``mira4_bait.xml`` (the Galaxy tool definition for mirabait) | |
| 49 * ``mira4.py`` (the Python wrapper script) | |
| 50 * ``mira4_convert.py`` (the Python wrapper script for miraconvert) | |
| 51 * ``mira4_bait.py`` (the Python wrapper script for mirabait) | |
| 52 * ``mira4_validator.py`` (the XML parameter validation script) | |
| 53 | |
| 54 The suggested location is a new ``tools/mira4_0`` folder. You will also need to | |
| 55 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool:: | |
| 56 | |
| 57 <tool file="mira4_0/mira4_de_novo.xml" /> | |
| 58 <tool file="mira4_0/mira4_mapping.xml" /> | |
| 59 ... | |
| 60 | |
| 61 You will also need to install MIRA, we used version 4.0.2, and define the | |
| 62 environment variable ``$MIRA4`` pointing at the folder containing the binaries. | |
| 63 See: | |
| 64 | |
| 65 * http://chevreux.org/projects_mira.html | |
| 66 * http://sourceforge.net/projects/mira-assembler/ | |
| 67 | |
| 68 You may wish to use different cluster setups for the de novo and mapping | |
| 69 tools, see above. | |
| 70 | |
| 71 You will also need to install samtools (for generating a BAM file from MIRA's | |
| 72 SAM output). | |
| 73 | |
| 74 If you wish to run the unit tests, also move/copy the ``test-data/`` files | |
| 75 under Galaxy's ``test-data/`` folder. Then:: | |
| 76 | |
| 77 $ ./run_tests.sh -id mira_4_0_bait | |
| 78 $ ./run_tests.sh -id mira_4_0_de_novo | |
| 79 $ ./run_tests.sh -id mira_4_0_mapping | |
| 80 $ ./run_tests.sh -id mira_4_0_convert | |
| 81 | |
| 82 | |
| 83 History | |
| 84 ======= | |
| 85 | |
| 86 ======= ====================================================================== | |
| 87 Version Changes | |
| 88 ------- ---------------------------------------------------------------------- | |
| 89 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4) | |
| 90 v0.0.2 - Include BAM output (using ``miraconvert`` and ``samtools``). | |
| 91 - Updated to target MIRA 4.0.1 | |
| 92 - Simplified XML to apply input format to output data. | |
| 93 - Sets temporary folder at run time to respect environment variables | |
| 94 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was | |
| 95 previously hard coded as ``/tmp``. | |
| 96 v0.0.3 - Updated to target MIRA 4.0.2 | |
| 97 v0.0.4 - Using ``optparse`` for the Python wrapper script API | |
| 98 - Made MAF and BAM outputs optional | |
| 99 - Include wrapper for ``miraconvert`` | |
| 100 v0.0.5 - Tool definition now embeds citation information. | |
| 101 v0.0.6 - Fixed error handling in ``mira4_convert.py``. | |
| 102 v0.0.7 - Renamed folder (internal change only). | |
| 103 - Reorder XML elements (internal change only). | |
| 104 - Use the ``format_source=...`` tag in the MIRA bait wrapper. | |
| 105 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
| 106 - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package. | |
| 107 v0.0.8 - Renamed folder now have a MIRA 4.9.x wrapper (internal change only). | |
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108 v0.0.9 - Additional unit tests now covering ``miraconvert``. |
| 4 | 109 - Re-include missing ``mirabait`` wrapper (accidentally left out when |
| 110 changed to using Planemo for uploading to the Tool Shed). | |
| 111 v0.0.10 - Python 3 compatible syntax (internal change only). | |
| 112 - Use ``<command detect_errors="aggressive">`` (internal change only). | |
| 113 - Single quote command line arguments (internal change only). | |
| 114 v0.0.11 - For compatibility with MIRA installed from the BioConda package, | |
| 115 if ``MIRA4$`` is not set, assume binaries are on the ``$PATH``. | |
| 2 | 116 ======= ====================================================================== |
| 117 | |
| 118 | |
| 119 Developers | |
| 120 ========== | |
| 121 | |
| 122 Development is on a dedicated GitHub repository: | |
|
3
a4f602cc3aa9
v0.0.9, was missing mirabait. Adds tests for miraconvert
peterjc
parents:
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diff
changeset
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123 https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 |
| 2 | 124 |
| 125 For pushing a release to the test or main "Galaxy Tool Shed", use the following | |
| 126 Planemo commands (which requires you have set your Tool Shed access details in | |
| 127 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
| 128 | |
|
3
a4f602cc3aa9
v0.0.9, was missing mirabait. Adds tests for miraconvert
peterjc
parents:
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diff
changeset
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129 $ planemo shed_update -t testtoolshed --check_diff tools/mira4_0/ |
| 2 | 130 ... |
| 131 | |
| 132 or:: | |
| 133 | |
|
3
a4f602cc3aa9
v0.0.9, was missing mirabait. Adds tests for miraconvert
peterjc
parents:
2
diff
changeset
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134 $ planemo shed_update -t toolshed --check_diff tools/mira4_0/ |
| 2 | 135 ... |
| 136 | |
| 137 To just build and check the tar ball, use:: | |
| 138 | |
|
3
a4f602cc3aa9
v0.0.9, was missing mirabait. Adds tests for miraconvert
peterjc
parents:
2
diff
changeset
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139 $ planemo shed_upload --tar_only tools/mira4_0/ |
| 2 | 140 ... |
| 141 $ tar -tzf shed_upload.tar.gz | |
| 142 test-data/U13small_m.fastq | |
| 143 ... | |
| 144 | |
| 145 | |
| 146 Licence (MIT) | |
| 147 ============= | |
| 148 | |
| 149 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 150 of this software and associated documentation files (the "Software"), to deal | |
| 151 in the Software without restriction, including without limitation the rights | |
| 152 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 153 copies of the Software, and to permit persons to whom the Software is | |
| 154 furnished to do so, subject to the following conditions: | |
| 155 | |
| 156 The above copyright notice and this permission notice shall be included in | |
| 157 all copies or substantial portions of the Software. | |
| 158 | |
| 159 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 160 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 161 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 162 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 163 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 164 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 165 THE SOFTWARE. |