Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4_0/README.rst @ 36:46d73b942b43 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65
| author | peterjc |
|---|---|
| date | Fri, 15 Sep 2017 10:09:14 -0400 |
| parents | 259891fce7fd |
| children |
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| 35:259891fce7fd | 36:46d73b942b43 |
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| 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. |
| 10 | 10 |
| 11 It is available from the Galaxy Tool Shed at: | 11 It is available from the Galaxy Tool Shed at: |
| 12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler | 12 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler |
| 13 | 13 |
| 14 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format, | 14 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format, |
| 15 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes | 15 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes |
| 16 | 16 |
| 17 A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at: | 17 A separate wrapper for MIRA v3.4 is available from the Galaxy Tool Shed at: |
| 36 Manual Installation | 36 Manual Installation |
| 37 =================== | 37 =================== |
| 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 various Python and XML files to install into Galaxy: | 43 There are various Python and XML files to install into Galaxy: |
| 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) |
| 136 | 136 |
| 137 To just build and check the tar ball, use:: | 137 To just build and check the tar ball, use:: |
| 138 | 138 |
| 139 $ planemo shed_upload --tar_only tools/mira4_0/ | 139 $ planemo shed_upload --tar_only tools/mira4_0/ |
| 140 ... | 140 ... |
| 141 $ tar -tzf shed_upload.tar.gz | 141 $ tar -tzf shed_upload.tar.gz |
| 142 test-data/U13small_m.fastq | 142 test-data/U13small_m.fastq |
| 143 ... | 143 ... |
| 144 | 144 |
| 145 | 145 |
| 146 Licence (MIT) | 146 Licence (MIT) |