Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4/README.rst @ 13:7fcabeeca5df draft

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Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
author peterjc
date Sun, 16 Feb 2014 16:30:48 -0500
parents a6a56440567c
children 133b863a8a40
comparison
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12:a6a56440567c 13:7fcabeeca5df
1 Galaxy wrapper for the MIRA assembly program (v4.0) 1 Galaxy wrapper for the MIRA assembly program (v4.0)
2 =================================================== 2 ===================================================
3 3
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence). 6 See the licence text below (MIT licence).
7 7
8 This tool is a short Python script (to collect the MIRA output and move it 8 This tool is a short Python script (to collect the MIRA output and move it
9 to where Galaxy expects the files) and associated Galaxy wrapper XML file. 9 to where Galaxy expects the files) and associated Galaxy wrapper XML file.
96 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 96 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
97 97
98 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 98 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
99 the following command from the Galaxy root folder:: 99 the following command from the Galaxy root folder::
100 100
101 $ 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 101 $ 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 test-data/empty_file.dat
102 102
103 Check this worked:: 103 Check this worked::
104 104
105 $ tar -tzf mira4_wrapper.tar.gz 105 $ tar -tzf mira4_wrapper.tar.gz
106 tools/mira4/README.rst 106 tools/mira4/README.rst
118 test-data/tvc_map_same_strain.fasta 118 test-data/tvc_map_same_strain.fasta
119 test-data/tvc_bait.fasta 119 test-data/tvc_bait.fasta
120 test-data/tvc_mini_bait_pos.fastq 120 test-data/tvc_mini_bait_pos.fastq
121 test-data/tvc_mini_bait_strict.fastq 121 test-data/tvc_mini_bait_strict.fastq
122 test-data/tvc_mini_bait_neg.fastq 122 test-data/tvc_mini_bait_neg.fastq
123 test-data/empty_file.dat
123 124
124 125
125 126
126 Licence (MIT) 127 Licence (MIT)
127 ============= 128 =============