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comparison tools/mira3/README.rst @ 11:e59904c855ae draft

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Uploaded v0.0.10, adds a test and updated download URL
author peterjc
date Wed, 30 Apr 2014 07:21:57 -0400
parents a2fb1e67bd11
children 63ebe9726219
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10:a2fb1e67bd11 11:e59904c855ae
15 15
16 Automated Installation 16 Automated Installation
17 ====================== 17 ======================
18 18
19 This should be straightforward, Galaxy should automatically download and 19 This should be straightforward, Galaxy should automatically download and
20 install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper, 20 install the precompiled binary for MIRA v3.4.1.1 for the Galaxy wrapper,
21 and run any tests. 21 and run any tests.
22 22
23 23
24 Manual Installation 24 Manual Installation
25 =================== 25 ===================
26 26
27 There are just two Galaxy files to install: 27 There are just two Galaxy files to install:
28 28
29 * mira.py (the Python script) 29 * ``mira.py`` (the Python script)
30 * mira.xml (the Galaxy tool definition) 30 * ``mira.xml`` (the Galaxy tool definition)
31 31
32 The suggested location is a new tools/mira3 folder. You will also need to 32 The suggested location is a new ``tools/mira3`` folder. You will also need to
33 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do 33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
34 this to tools_conf.xml.sample in order to run any tests:: 34 this to ``tools_conf.xml.sample`` in order to run any tests::
35 35
36 <tool file="mira3/mira.xml" /> 36 <tool file="mira3/mira.xml" />
37 37
38 You will also need to install MIRA, we used version 3.4.1.1. See: 38 You will also need to install MIRA, we used version 3.4.1.1. See:
39 39
72 - Use reStructuredText for this README file. 72 - Use reStructuredText for this README file.
73 - Adopted standard MIT licence. 73 - Adopted standard MIT licence.
74 - Updated citation information (Cock et al. 2013). 74 - Updated citation information (Cock et al. 2013).
75 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 75 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
76 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper). 76 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
77 - Correct path issue in automated dependency installation 77 - Correct path issue in automated dependency installation.
78 v0.0.10 - Added a functional test.
79 - Updated URL for automated installation of MIRA v3.4.1.1
78 ======= ====================================================================== 80 ======= ======================================================================
79 81
80 82
81 Developers 83 Developers
82 ========== 84 ==========
88 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4 90 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
89 91
90 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 92 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
91 the following command from the Galaxy root folder:: 93 the following command from the Galaxy root folder::
92 94
93 $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta 95 $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat
94 96
95 Check this worked:: 97 Check this worked::
96 98
97 $ tar -tzf mira3_wrapper.tar.gz 99 $ tar -tzf mira3_wrapper.tar.gz
98 tools/mira3/README.rst 100 tools/mira3/README.rst
99 tools/mira3/mira.xml 101 tools/mira3/mira.xml
100 tools/mira3/mira.py 102 tools/mira3/mira.py
101 tools/mira3/tool_dependencies.xml 103 tools/mira3/tool_dependencies.xml
102 test-data/tvc_mini.fastq 104 test-data/tvc_mini.fastq
103 test-data/tvc_contigs.fasta 105 test-data/tvc_contigs.fasta
106 test-data/empty_file.dat
104 107
105 108
106 Licence (MIT) 109 Licence (MIT)
107 ============= 110 =============
108 111