Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4/README.rst @ 4:df86ed992a1b draft

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Uploaded preview 4, lots of work on mapping
author peterjc
date Fri, 11 Oct 2013 04:28:45 -0400
parents c7538ae82a24
children ffefb87bd414
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3:c7538ae82a24 4:df86ed992a1b
35 35
36 First install the 'mira' datatype for Galaxy, available here: 36 First install the 'mira' datatype for Galaxy, available here:
37 37
38 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes 38 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
39 39
40 There are just two Galaxy files to install: 40 There are just three Galaxy files to install:
41 41
42 * mira4.py (the Python script) 42 * mira4.py (the Python script)
43 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage) 43 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage)
44 * mira4_mapping.xml (the Galaxy tool definition for mapping usage) 44 * mira4_mapping.xml (the Galaxy tool definition for mapping usage)
45 45
48 this to tools_conf.xml.sample in order to run any tests:: 48 this to tools_conf.xml.sample in order to run any tests::
49 49
50 <tool file="mira4/mira4_de_novo.xml" /> 50 <tool file="mira4/mira4_de_novo.xml" />
51 <tool file="mira4/mira4_mapping.xml" /> 51 <tool file="mira4/mira4_mapping.xml" />
52 52
53 You will also need to install MIRA, we used version 4.0 RC2. See: 53 You will also need to install MIRA, we used version 4.0 RC3. See:
54 54
55 * http://chevreux.org/projects_mira.html 55 * http://chevreux.org/projects_mira.html
56 * http://sourceforge.net/projects/mira-assembler/ 56 * http://sourceforge.net/projects/mira-assembler/
57 57
58 You may wish to use different cluster setups for the de novo and mapping 58 You may wish to use different cluster setups for the de novo and mapping
63 ======= 63 =======
64 64
65 ======= ====================================================================== 65 ======= ======================================================================
66 Version Changes 66 Version Changes
67 ------- ---------------------------------------------------------------------- 67 ------- ----------------------------------------------------------------------
68 v0.0.1 - Initial version (prototype using MIRA 4.0 RC2, and wrapper for v3.4) 68 v0.0.1 - Initial version (prototype for MIRA 4.0 RC3, based on wrapper for v3.4)
69 ======= ====================================================================== 69 ======= ======================================================================
70 70
71 71
72 Developers 72 Developers
73 ========== 73 ==========
74 74
75 Development is on a dedicated GitHub repository: 75 Development is on a dedicated GitHub repository:
76 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0 76 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
77 77
78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
79 the following command from the Galaxy root folder:: 79 the following command from the Galaxy root folder::
80 80
81 $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs_mira4.fasta 81 $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4.py tools/mira4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta
82 82
83 Check this worked:: 83 Check this worked::
84 84
85 $ tar -tzf mira4_wrapper.tar.gz 85 $ tar -tzf mira4_wrapper.tar.gz
86 tools/mira4/README.rst 86 tools/mira4/README.rst
87 tools/mira4/mira4_de_novo.xml 87 tools/mira4/mira4_de_novo.xml
88 tools/mira4/mira4_mapping.xml 88 tools/mira4/mira4_mapping.xml
89 tools/mira4/mira4.py 89 tools/mira4/mira4.py
90 tools/mira4/tool_dependencies.xml 90 tools/mira4/tool_dependencies.xml
91 test-data/tvc_mini.fastq 91 test-data/tvc_mini.fastq
92 test-data/tvc_contigs_mira4.fasta 92 test-data/tvc_contigs.fasta
93 test-data/tvc_map_ref_strain.fasta
94 test-data/tvc_map_same_strain.fasta
93 95
94 96
95 Licence (MIT) 97 Licence (MIT)
96 ============= 98 =============
97 99