Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4/README.rst @ 6:626d5cfd01aa draft
Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
| author | peterjc |
|---|---|
| date | Mon, 21 Oct 2013 12:01:47 -0400 |
| parents | ffefb87bd414 |
| children | 902f01c1084b |
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| 5:ffefb87bd414 | 6:626d5cfd01aa |
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| 38 | 38 |
| 39 First install the 'mira' datatype for Galaxy, available here: | 39 First install the 'mira' datatype for Galaxy, available here: |
| 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 just three Galaxy files to install: | 43 There are four Galaxy files to install: |
| 44 | 44 |
| 45 * mira4.py (the Python script) | 45 * mira4.py (the Python wrapper script) |
| 46 * mira4_validator.py (the Python parameter validation script) | |
| 46 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage) | 47 * mira4_de_novo.xml (the Galaxy tool definition for de novo usage) |
| 47 * mira4_mapping.xml (the Galaxy tool definition for mapping usage) | 48 * mira4_mapping.xml (the Galaxy tool definition for mapping usage) |
| 48 | 49 |
| 49 The suggested location is a new tools/mira4 folder. You will also need to | 50 The suggested location is a new tools/mira4 folder. You will also need to |
| 50 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do | 51 modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do |
| 79 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 | 80 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4 |
| 80 | 81 |
| 81 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | 82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
| 82 the following command from the Galaxy root folder:: | 83 the following command from the Galaxy root folder:: |
| 83 | 84 |
| 84 $ 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 | 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 |
| 85 | 86 |
| 86 Check this worked:: | 87 Check this worked:: |
| 87 | 88 |
| 88 $ tar -tzf mira4_wrapper.tar.gz | 89 $ tar -tzf mira4_wrapper.tar.gz |
| 89 tools/mira4/README.rst | 90 tools/mira4/README.rst |
| 90 tools/mira4/mira4_de_novo.xml | 91 tools/mira4/mira4_de_novo.xml |
| 91 tools/mira4/mira4_mapping.xml | 92 tools/mira4/mira4_mapping.xml |
| 92 tools/mira4/mira4.py | 93 tools/mira4/mira4.py |
| 94 tools/mira4/mira4_validator.py | |
| 93 tools/mira4/tool_dependencies.xml | 95 tools/mira4/tool_dependencies.xml |
| 94 test-data/tvc_mini.fastq | 96 test-data/tvc_mini.fastq |
| 95 test-data/tvc_contigs.fasta | 97 test-data/tvc_contigs.fasta |
| 96 test-data/tvc_map_ref_strain.fasta | 98 test-data/tvc_map_ref_strain.fasta |
| 97 test-data/tvc_map_same_strain.fasta | 99 test-data/tvc_map_same_strain.fasta |