Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4/README.rst @ 19:8487d70e82aa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.3 preview 1, target MIRA v4.0.2
author peterjc
date Wed, 21 May 2014 06:56:06 -0400
parents 381aa262c8cb
children aeb3e35f8236
comparison
equal deleted inserted replaced
18:381aa262c8cb 19:8487d70e82aa
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 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.
30 30
54 this to ``tools_conf.xml.sample`` in order to run the tests:: 54 this to ``tools_conf.xml.sample`` in order to run the tests::
55 55
56 <tool file="mira4/mira4_de_novo.xml" /> 56 <tool file="mira4/mira4_de_novo.xml" />
57 <tool file="mira4/mira4_mapping.xml" /> 57 <tool file="mira4/mira4_mapping.xml" />
58 58
59 You will also need to install MIRA, we used version 4.0, and define the 59 You will also need to install MIRA, we used version 4.0.2, and define the
60 environment variable ``$MIRA4`` pointing at the folder containing the binaries. 60 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
61 See: 61 See:
62 62
63 * http://chevreux.org/projects_mira.html 63 * http://chevreux.org/projects_mira.html
64 * http://sourceforge.net/projects/mira-assembler/ 64 * http://sourceforge.net/projects/mira-assembler/
83 ======= ====================================================================== 83 ======= ======================================================================
84 Version Changes 84 Version Changes
85 ------- ---------------------------------------------------------------------- 85 ------- ----------------------------------------------------------------------
86 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4) 86 v0.0.1 - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
87 v0.0.2 - Include BAM output (using ``miraconvert`` and ``samtools``). 87 v0.0.2 - Include BAM output (using ``miraconvert`` and ``samtools``).
88 - Updated to target MIRA 4.0 88 - Updated to target MIRA 4.0.1
89 - Simplified XML to apply input format to output data. 89 - Simplified XML to apply input format to output data.
90 - Sets temporary folder at run time to respect environment variables 90 - Sets temporary folder at run time to respect environment variables
91 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was 91 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
92 previously hard coded as ``/tmp``. 92 previously hard coded as ``/tmp``.
93 v0.0.3 - Updated to target MIRA 4.0.2
93 ======= ====================================================================== 94 ======= ======================================================================
94 95
95 96
96 Developers 97 Developers
97 ========== 98 ==========