Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4/README.rst @ 7:902f01c1084b draft
Uploaded v0.0.1 preview 7, with mirabait wrapper
| author | peterjc |
|---|---|
| date | Fri, 25 Oct 2013 07:18:38 -0400 (2013-10-25) |
| parents | 626d5cfd01aa |
| children | 302d13490b23 |
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| 6:626d5cfd01aa | 7:902f01c1084b |
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| 52 this to tools_conf.xml.sample in order to run any tests:: | 52 this to tools_conf.xml.sample in order to run any tests:: |
| 53 | 53 |
| 54 <tool file="mira4/mira4_de_novo.xml" /> | 54 <tool file="mira4/mira4_de_novo.xml" /> |
| 55 <tool file="mira4/mira4_mapping.xml" /> | 55 <tool file="mira4/mira4_mapping.xml" /> |
| 56 | 56 |
| 57 You will also need to install MIRA, we used version 4.0 RC4. See: | 57 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. | |
| 59 See: | |
| 58 | 60 |
| 59 * http://chevreux.org/projects_mira.html | 61 * http://chevreux.org/projects_mira.html |
| 60 * http://sourceforge.net/projects/mira-assembler/ | 62 * http://sourceforge.net/projects/mira-assembler/ |
| 61 | 63 |
| 62 You may wish to use different cluster setups for the de novo and mapping | 64 You may wish to use different cluster setups for the de novo and mapping |
| 80 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 | 82 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 |
| 81 | 83 |
| 82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | 84 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
| 83 the following command from the Galaxy root folder:: | 85 the following command from the Galaxy root folder:: |
| 84 | 86 |
| 85 $ 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 | 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 |
| 86 | 88 |
| 87 Check this worked:: | 89 Check this worked:: |
| 88 | 90 |
| 89 $ tar -tzf mira4_wrapper.tar.gz | 91 $ tar -tzf mira4_wrapper.tar.gz |
| 90 tools/mira4/README.rst | 92 tools/mira4/README.rst |
| 95 tools/mira4/tool_dependencies.xml | 97 tools/mira4/tool_dependencies.xml |
| 96 test-data/tvc_mini.fastq | 98 test-data/tvc_mini.fastq |
| 97 test-data/tvc_contigs.fasta | 99 test-data/tvc_contigs.fasta |
| 98 test-data/tvc_map_ref_strain.fasta | 100 test-data/tvc_map_ref_strain.fasta |
| 99 test-data/tvc_map_same_strain.fasta | 101 test-data/tvc_map_same_strain.fasta |
| 102 test-data/tvc_bait.fasta | |
| 103 test-data/tvc_mini_bait_pos.fastq | |
| 104 test-data/tvc_mini_bait_strict.fastq | |
| 105 test-data/tvc_mini_bait_neg.fastq | |
| 106 | |
| 100 | 107 |
| 101 | 108 |
| 102 Licence (MIT) | 109 Licence (MIT) |
| 103 ============= | 110 ============= |
| 104 | 111 |