Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4/README.rst @ 21:4abe8d59a438 draft

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Uploaded v0.0.4 preview 1; fix getting BAM without MAF
author peterjc
date Tue, 28 Oct 2014 08:29:59 -0400
parents aeb3e35f8236
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20:aeb3e35f8236 21:4abe8d59a438
42 42
43 There are four Galaxy files to install: 43 There are four Galaxy files to install:
44 44
45 * ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage) 45 * ``mira4_de_novo.xml`` (the Galaxy tool definition for de novo usage)
46 * ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage) 46 * ``mira4_mapping.xml`` (the Galaxy tool definition for mapping usage)
47 * ``mira4_convert.xml`` (the Galaxy tool definition for converting MIRA files)
47 * ``mira4_bait.xml`` (the Galaxy tool definition for mirabait) 48 * ``mira4_bait.xml`` (the Galaxy tool definition for mirabait)
48 * ``mira4.py`` (the Python wrapper script) 49 * ``mira4.py`` (the Python wrapper script)
49 * ``mira_bait.py`` (the Python wrapper script for mirabait) 50 * ``mira4_convert.py`` (the Python wrapper script for miraconvert)
51 * ``mira4_bait.py`` (the Python wrapper script for mirabait)
50 * ``mira4_validator.py`` (the XML parameter validation script) 52 * ``mira4_validator.py`` (the XML parameter validation script)
51 53
52 The suggested location is a new ``tools/mira4`` folder. You will also need to 54 The suggested location is a new ``tools/mira4`` folder. You will also need to
53 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do 55 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
54 this to ``tools_conf.xml.sample`` in order to run the tests:: 56 this to ``tools_conf.xml.sample`` in order to run the tests::
73 folder, you can run the tests with:: 75 folder, you can run the tests with::
74 76
75 $ ./run_functional_tests.sh -id mira_4_0_bait 77 $ ./run_functional_tests.sh -id mira_4_0_bait
76 $ ./run_functional_tests.sh -id mira_4_0_de_novo 78 $ ./run_functional_tests.sh -id mira_4_0_de_novo
77 $ ./run_functional_tests.sh -id mira_4_0_mapping 79 $ ./run_functional_tests.sh -id mira_4_0_mapping
80 $ ./run_functional_tests.sh -id mira_4_0_convert
78 81
79 82
80 History 83 History
81 ======= 84 =======
82 85
91 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was 94 (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
92 previously hard coded as ``/tmp``. 95 previously hard coded as ``/tmp``.
93 v0.0.3 - Updated to target MIRA 4.0.2 96 v0.0.3 - Updated to target MIRA 4.0.2
94 v0.0.4 - Using optparse for the Python wrapper script API 97 v0.0.4 - Using optparse for the Python wrapper script API
95 - Made MAF and BAM outputs optional 98 - Made MAF and BAM outputs optional
99 - Include wrapper for ``miraconvert``
96 ======= ====================================================================== 100 ======= ======================================================================
97 101
98 102
99 Developers 103 Developers
100 ========== 104 ==========
103 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 107 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
104 108
105 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 109 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
106 the following command from the Galaxy root folder:: 110 the following command from the Galaxy root folder::
107 111
108 $ 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 tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta 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 test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/empty_file.dat 112 $ 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_convert.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_convert.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta 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 test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/header.mira test-data/empty_file.dat
109 113
110 Check this worked:: 114 Check this worked::
111 115
112 $ tar -tzf mira4_wrapper.tar.gz 116 $ tar -tzf mira4_wrapper.tar.gz
113 tools/mira4/README.rst 117 tools/mira4/README.rst
114 tools/mira4/mira4_de_novo.xml 118 tools/mira4/mira4_de_novo.xml
115 tools/mira4/mira4_mapping.xml 119 tools/mira4/mira4_mapping.xml
116 tools/mira4/mira4_bait.xml 120 tools/mira4/mira4_bait.xml
121 tools/mira4/mira4_convert.xml
117 tools/mira4/mira4.py 122 tools/mira4/mira4.py
118 tools/mira4/mira4_make_bam.py 123 tools/mira4/mira4_make_bam.py
119 tools/mira4/mira4_validator.py 124 tools/mira4/mira4_validator.py
125 tools/mira4/mira4_convert.py
120 tools/mira4/mira4_bait.py 126 tools/mira4/mira4_bait.py
121 tools/mira4/tool_dependencies.xml 127 tools/mira4/tool_dependencies.xml
122 tools/mira4/repository_dependencies.xml 128 tools/mira4/repository_dependencies.xml
123 test-data/U13small_m.fastq 129 test-data/U13small_m.fastq
124 test-data/U13small_m.mira4_de_novo.fasta 130 test-data/U13small_m.mira4_de_novo.fasta
130 test-data/tvc_mini_bait_pos.fastq 136 test-data/tvc_mini_bait_pos.fastq
131 test-data/tvc_mini_bait_strict.fastq 137 test-data/tvc_mini_bait_strict.fastq
132 test-data/tvc_mini_bait_neg.fastq 138 test-data/tvc_mini_bait_neg.fastq
133 test-data/ecoli.fastq 139 test-data/ecoli.fastq
134 test-data/ecoli.mira4_de_novo.fasta 140 test-data/ecoli.mira4_de_novo.fasta
141 test-data/header.mira
135 test-data/empty_file.dat 142 test-data/empty_file.dat
136 143
137 144
138 145
139 Licence (MIT) 146 Licence (MIT)