Mercurial > repos > peterjc > mira4_9_mirabait

annotate tools/mira4_9/mirabait/README.rst @ 1:33bfaf5865c5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit cd0ab853082e608d5646638b2d46489480616436
author peterjc
date Tue, 13 Oct 2015 10:01:25 -0400
parents 5979f13c2dc5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
1 Galaxy wrapper for the MIRA assembly program (v4.9) mirabait
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
2 ============================================================
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
3
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
6 See the licence text below (MIT licence).
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
7
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
8 This is a Galaxy wrapper for ``mirabait`` from the MIRA 4.9 assembly suite.
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
9
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
10 It is available from the Galaxy Tool Shed at:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
11 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
12
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
13 Development/test previews are available from the Galaxy Test Tool Shed at:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
14 http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
15
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
16 It is part of a suite for all the MIRA 4.9 tools:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
17 TODO...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
18
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
19 A separate wrapper for MIRA v4.0 is available from the Galaxy Tool Shed at:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
20 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
21
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
22
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
23 Automated Installation
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
24 ======================
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
25
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
26 This should be straightforward. Via the Tool Shed, Galaxy should automatically
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
27 install the precompiled binaries for MIRA v4.9.5, and offer to run any tests.
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
28
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
29
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
30 Manual Installation
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
31 ===================
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
32
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
33 There are various Python and XML files to install into Galaxy:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
34
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
35 * ``mira4_9_mirabait.xml`` (the Galaxy tool definition for mirabait)
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
36 * ``mira_check_version.py`` (Python helper script)
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
37
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
38 The suggested location is a new ``tools/mira4_9`` folder. You will
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
39 also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
40 tool::
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
41
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
42 <tool file="mira4_9/mirabait/mira4_9_mirabait.xml" />
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
43 ...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
44
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
45 You will also need to install MIRA 4.9, we used version 4.9.5, and define the
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
46 environment variable ``$MIRA4_9`` pointing at the folder containing the
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
47 binaries. See:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
48
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
49 * http://chevreux.org/projects_mira.html
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
50 * http://sourceforge.net/projects/mira-assembler/
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
51
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
52 You may wish to use different cluster setups for the de novo and mapping
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
53 tools, see above.
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
54
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
55 You will also need to install samtools (for generating a BAM file from MIRA's
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
56 SAM output).
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
57
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
58 If you wish to run the unit tests, also move/copy the ``test-data/`` files
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
59 under Galaxy's ``test-data/`` folder. Then::
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
60
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
61 $ ./run_tests.sh -id mira4_9_mirabait
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
62 ...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
63
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
64
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
65 History
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
66 =======
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
67
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
68 ======= ======================================================================
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
69 Version Changes
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
70 ------- ----------------------------------------------------------------------
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
71 v0.0.1 - Initial version for MIRA 4.9.5, based on wrapper for v4.0.2
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
72 ======= ======================================================================
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
73
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
74
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
75 Developers
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
76 ==========
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
77
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
78 Development is on a dedicated GitHub repository:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
79 https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
80
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
81 For pushing a release to the test or main "Galaxy Tool Shed", use the following
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
82 Planemo commands (which requires you have set your Tool Shed access details in
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
83 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
84
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
85 $ planemo shed_update -t testtoolshed --check_diff tools/mira4_9/
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
86 ...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
87
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
88 or::
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
89
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
90 $ planemo shed_update -t toolshed --check_diff tools/mira4_9/
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
91 ...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
92
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
93 To just build and check the tar ball, use::
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
94
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
95 $ planemo shed_upload --tar_only mira4_9/
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
96 ...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
97 $ tar -tzf shed_upload.tar.gz
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
98 ...
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
99
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
100
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
101 Licence (MIT)
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
102 =============
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
103
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
104 Permission is hereby granted, free of charge, to any person obtaining a copy
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
105 of this software and associated documentation files (the "Software"), to deal
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
106 in the Software without restriction, including without limitation the rights
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
108 copies of the Software, and to permit persons to whom the Software is
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
109 furnished to do so, subject to the following conditions:
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
110
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
111 The above copyright notice and this permission notice shall be included in
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
112 all copies or substantial portions of the Software.
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
113
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
5979f13c2dc5 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
parents:
diff changeset
120 THE SOFTWARE.