Mercurial > repos > peterjc > mira_datatypes

comparison README.rst @ 1:54318d4bcadd draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit 6c847766578b830749971753148246101bbe0983
author peterjc
date Tue, 15 Sep 2015 09:43:39 -0400
parents 29ff2a2b6eaa
children 2b5ff55127c3
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0:29ff2a2b6eaa 1:54318d4bcadd
38 Manual Installation 38 Manual Installation
39 =================== 39 ===================
40 40
41 Normally you would install this via the Galaxy ToolShed, which would move 41 Normally you would install this via the Galaxy ToolShed, which would move
42 the provided mira.py file into a suitable location and process the 42 the provided mira.py file into a suitable location and process the
43 datatypes_conf.xml entry to be combined with your local configuration. 43 ``datatypes_conf.xml`` entry to be combined with your local configuration.
44 44
45 However, if you really want to this should work for a manual install. Add 45 However, if you really want to this should work for a manual install. Add
46 the following lines to the datatypes_conf.xml file in the Galaxy main folder:: 46 the following lines to the ``datatypes_conf.xml`` file in the Galaxy main folder::
47 47
48 <datatype extension="mira" type="galaxy.datatypes.mira:MiraAssemblyFormat" mimetype="text/plain" display_in_upload="true"/> 48 <datatype extension="mira" type="galaxy.datatypes.mira:MiraAssemblyFormat" mimetype="text/plain" display_in_upload="true"/>
49 49
50 and later in the sniffer section:: 50 and later in the sniffer section::
51 51
52 <sniffer type="galaxy.datatypes.mira:MiraAssemblyFormat"/> 52 <sniffer type="galaxy.datatypes.mira:MiraAssemblyFormat"/>
53 53
54 Also create the file lib/galaxy/datatypes/mira.py by moving, copying or linking 54 Also create the file ``lib/galaxy/datatypes/mira.py`` by moving, copying or linking
55 the mira.py file provided in this tar-ball. Finally add 'import mira' near 55 the mira.py file provided in this tar-ball. Finally add ``import mira`` near
56 the start of file lib/galaxy/datatypes/registry.py (after the other import 56 the start of file ``lib/galaxy/datatypes/registry.py`` (after the other import
57 lines). 57 lines).
58 58
59 59
60 Bug Reports 60 Bug Reports
61 =========== 61 ===========
69 69
70 Development is done on this GitHub repository: 70 Development is done on this GitHub repository:
71 https://github.com/peterjc/pico_galaxy 71 https://github.com/peterjc/pico_galaxy
72 72
73 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use 73 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
74 the following command from the mira_datatypes folder:: 74 the following command from the ``mira_datatypes`` folder::
75 75
76 $ tar -czf mira_datatypes.tar.gz README.rst datatypes_conf.xml mira.py 76 $ tar -czf mira_datatypes.tar.gz README.rst datatypes_conf.xml mira.py
77 77
78 Check this worked:: 78 Check this worked::
79 79
81 README.rst 81 README.rst
82 datatypes_conf.xml 82 datatypes_conf.xml
83 mira.py 83 mira.py
84 84
85 For development, rather than having a local ToolShed running, I currently 85 For development, rather than having a local ToolShed running, I currently
86 use a symlink from lib/galaxy/datatypes/mira.py to the actual file as 86 use a symlink from ``lib/galaxy/datatypes/mira.py`` to the actual file as
87 described above. 87 described above.
88 88
89 89
90 Licence (MIT) 90 Licence (MIT)
91 ============= 91 =============