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comparison tools/mira4/README.rst @ 9:302d13490b23 draft

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Uploaded v0.0.2 preview 1, BAM output
author peterjc
date Thu, 28 Nov 2013 05:07:59 -0500
parents 902f01c1084b
children 02350bef2e99
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8:2ab1d6f6a8ec 9:302d13490b23
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, download and install the precompiled binary for 24 install the 'mira' datatype, samtools, and download and install the precompiled
25 MIRA v4.0 for the Galaxy wrapper, and run any tests. 25 binary for MIRA v4.0 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
40 40
41 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes 41 * http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
42 42
43 There are four Galaxy files to install: 43 There are four Galaxy files to install:
44 44
45 * mira4.py (the Python wrapper script) 45 * ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage)
46 * mira4_validator.py (the Python parameter validation script) 46 * ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
47 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage) 47 * ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
48 * mira4_mapping.xml (the Galaxy tool definition for mapping usage) 48 * ``mira4.py`` (the Python wrapper script)
49 * ``mira_bait.py`` (the Python wrapper script for mirabait)
50 * ``mira4_validator.py`` (the XML parameter validation script)
49 51
50 The suggested location is a new tools/mira4 folder. You will also need to 52 The suggested location is a new ``tools/mira4`` folder. You will also need to
51 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do 53 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
52 this to tools_conf.xml.sample in order to run any tests:: 54 this to ``tools_conf.xml.sample`` in order to run the tests::
53 55
54 <tool file="mira4/mira4_de_novo.xml" /> 56 <tool file="mira4/mira4_de_novo.xml" />
55 <tool file="mira4/mira4_mapping.xml" /> 57 <tool file="mira4/mira4_mapping.xml" />
56 58
57 You will also need to install MIRA, we used version 4.0 RC4, and define the 59 You will also need to install MIRA, we used version 4.0 RC4, and define the
58 environment variable $MIRA4 pointing at the folder containing the binaries. 60 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
59 See: 61 See:
60 62
61 * http://chevreux.org/projects_mira.html 63 * http://chevreux.org/projects_mira.html
62 * http://sourceforge.net/projects/mira-assembler/ 64 * http://sourceforge.net/projects/mira-assembler/
63 65
64 You may wish to use different cluster setups for the de novo and mapping 66 You may wish to use different cluster setups for the de novo and mapping
65 tools, see above. 67 tools, see above.
68
69 You will also need to install samtools (for generating a BAM file from MIRA's
70 SAM output).
71
72 After copying (or symlinking) the ``test-data`` files under Galaxy's ``test-data``
73 folder, you can run the tests with::
74
75 $ ./run_functional_tests.sh -id mira_4_0_bait
76 $ ./run_functional_tests.sh -id mira_4_0_de_novo
77 $ ./run_functional_tests.sh -id mira_4_0_mapping
66 78
67 79
68 History 80 History
69 ======= 81 =======
70 82
71 ======= ====================================================================== 83 ======= ======================================================================
72 Version Changes 84 Version Changes
73 ------- ---------------------------------------------------------------------- 85 ------- ----------------------------------------------------------------------
74 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``).
75 ======= ====================================================================== 88 ======= ======================================================================
76 89
77 90
78 Developers 91 Developers
79 ========== 92 ==========
82 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 95 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
83 96
84 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 97 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
85 the following command from the Galaxy root folder:: 98 the following command from the Galaxy root folder::
86 99
87 $ 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/mira4_validator.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 test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq 100 $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_bait.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 test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq
88 101
89 Check this worked:: 102 Check this worked::
90 103
91 $ tar -tzf mira4_wrapper.tar.gz 104 $ tar -tzf mira4_wrapper.tar.gz
92 tools/mira4/README.rst 105 tools/mira4/README.rst
93 tools/mira4/mira4_de_novo.xml 106 tools/mira4/mira4_de_novo.xml
94 tools/mira4/mira4_mapping.xml 107 tools/mira4/mira4_mapping.xml
108 tools/mira4/mira4_bait.xml
95 tools/mira4/mira4.py 109 tools/mira4/mira4.py
110 tools/mira4/mira4_make_bam.py
96 tools/mira4/mira4_validator.py 111 tools/mira4/mira4_validator.py
112 tools/mira4/mira4_bait.py
97 tools/mira4/tool_dependencies.xml 113 tools/mira4/tool_dependencies.xml
98 test-data/tvc_mini.fastq 114 test-data/tvc_mini.fastq
99 test-data/tvc_contigs.fasta 115 test-data/tvc_contigs.fasta
100 test-data/tvc_map_ref_strain.fasta 116 test-data/tvc_map_ref_strain.fasta
101 test-data/tvc_map_same_strain.fasta 117 test-data/tvc_map_same_strain.fasta