Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/README.rst @ 36:46d73b942b43 draft

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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
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35:259891fce7fd 36:46d73b942b43
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)