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comparison tools/mira4_0/README.rst @ 32:56b421d59805 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
author peterjc
date Thu, 18 May 2017 13:36:08 -0400
parents b506e3b779fa
children 259891fce7fd
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31:fd95aaef8818 32:56b421d59805
1 Galaxy wrapper for the MIRA assembly program (v4.0) 1 Galaxy wrapper for the MIRA assembly program (v4.0)
2 =================================================== 2 ===================================================
3 3
4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2011-2016 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence). 6 See the licence text below (MIT licence).
7 7
8 This tool is a short Python script (to collect the MIRA output and move it 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. 9 to where Galaxy expects the files) and associated Galaxy wrapper XML file.
19 19
20 Automated Installation 20 Automated Installation
21 ====================== 21 ======================
22 22
23 This should be straightforward. Via the Tool Shed, Galaxy should automatically 23 This should be straightforward. Via the Tool Shed, Galaxy should automatically
24 install the ``mira`` datatype, samtools, and download and install the precompiled 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. 25 binary for MIRA v4.0.2 for the Galaxy wrapper, and run any tests.
26 26
27 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate 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). 28 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
29 Consult the Galaxy adminstration documentation for your cluster setup. 29 Consult the Galaxy adminstration documentation for your cluster setup.
104 - Use the ``format_source=...`` tag in the MIRA bait wrapper. 104 - Use the ``format_source=...`` tag in the MIRA bait wrapper.
105 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 105 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
106 - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package. 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). 107 v0.0.8 - Renamed folder now have a MIRA 4.9.x wrapper (internal change only).
108 v0.0.9 - Additional unit tests now covering ``miraconvert``. 108 v0.0.9 - Additional unit tests now covering ``miraconvert``.
109 - Was missing ``mirabait`` wrapper since move to using Planemo. 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).
110 ======= ====================================================================== 114 ======= ======================================================================
111 115
112 116
113 Developers 117 Developers
114 ========== 118 ==========