Mercurial > repos > peterjc > mira_assembler

annotate tools/mira3/README.rst @ 17:557118c7e29e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 3c6f0dca0e1318eecd1e07d177ffc5752b4f6c95
author peterjc
date Thu, 21 May 2015 10:52:16 -0400
parents f74bc0420db4
children 082d6adb57a5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
1 Galaxy wrapper for the MIRA assembly program (v3.4)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
2 ===================================================
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
3
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
6 See the licence text below (MIT licence).
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
7
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
8 This tool is a short Python script (to collect the MIRA output and move it
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
10 separated file for use in Galaxy).
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
11
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
12 It is available from the Galaxy Tool Shed at:
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
13 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
14
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
15
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
16 Automated Installation
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
17 ======================
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
18
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
19 This should be straightforward, Galaxy should automatically download and
15
fbe9139eb74b Uploaded v0.0.10b, updated download URL
peterjc
parents: 14
diff changeset
20 install the precompiled binary for MIRA v3.4.1.1 for the Galaxy wrapper,
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
21 and run any tests.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
22
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
23
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
24 Manual Installation
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
25 ===================
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
26
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
27 There are just two Galaxy files to install:
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
28
13
8a05c6b852c3 Uploaded v0.0.10, adding test
peterjc
parents: 12
diff changeset
29 * ``mira.py`` (the Python script)
8a05c6b852c3 Uploaded v0.0.10, adding test
peterjc
parents: 12
diff changeset
30 * ``mira.xml`` (the Galaxy tool definition)
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
31
13
8a05c6b852c3 Uploaded v0.0.10, adding test
peterjc
parents: 12
diff changeset
32 The suggested location is a new ``tools/mira3`` folder. You will also need to
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
34 the line::
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
35
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
36 <tool file="mira3/mira.xml" />
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
37
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
38 If you wish to run the unit tests, also move/copy the ``test-data/`` files
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
39 under Galaxy's ``test-data/`` folder. Then::
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
40
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
41 $ ./run_tests -id mira_assembler
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
42
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
43 You will also need to install MIRA, we used version 3.4.1.1. See:
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
44
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
45 * http://chevreux.org/projects_mira.html
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
46 * http://sourceforge.net/projects/mira-assembler/
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
47
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
48 WARNING: This tool was initially developed to construct viral genome assembly
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
49 and mapping pipelines, for which the run time and memory requirements are
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
50 negligible. For larger tasks, be aware that MIRA can require vast amounts
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
51 of RAM and run-times of over a week are possible. This tool wrapper makes
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
52 no attempt to spot and reject such large jobs.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
53
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
54
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
55 History
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
56 =======
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
57
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
58 ======= ======================================================================
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
59 Version Changes
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
60 ------- ----------------------------------------------------------------------
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
61 v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
62 v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
63 v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
64 (some other switches changed, e.g. -OUT rrol to rrot, which
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
65 means the wrapper no longer works with MIRA 3.2.x)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
66 - The contig summary file (TCS file) was removed in MIRA 3.4
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
67 - Report all missing output files (not just first missing one)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
68 v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
69 v0.0.5 - Implement the <version_command> tag to record the wrapper
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
70 version and the MIRA version being used.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
71 - Check using MIRA 3.4 (later versions have a different API)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
72 v0.0.6 - Tell MIRA to use /tmp for temporary files
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
73 - Tell MIRA to ignore long read names (otherwise it aborts)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
74 v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
75 v0.0.8 - Basic unit test added (but commented out due to Galaxy issue).
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
76 - Link to Tool Shed added to help text and this documentation.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
77 - Use reStructuredText for this README file.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
78 - Adopted standard MIT licence.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
79 - Updated citation information (Cock et al. 2013).
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
80 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
81 v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
13
8a05c6b852c3 Uploaded v0.0.10, adding test
peterjc
parents: 12
diff changeset
82 - Correct path issue in automated dependency installation.
8a05c6b852c3 Uploaded v0.0.10, adding test
peterjc
parents: 12
diff changeset
83 v0.0.10 - Added a functional test.
15
fbe9139eb74b Uploaded v0.0.10b, updated download URL
peterjc
parents: 14
diff changeset
84 - Updated URL for automated installation of MIRA v3.4.1.1
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
85 v0.0.11 - Tool definition now embeds citation information.
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
87 ======= ======================================================================
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
88
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
89
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
90 Developers
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
91 ==========
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
92
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
93 This script and related tools were initially developed on the following hg branch:
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
94 http://bitbucket.org/peterjc/galaxy-central/src/tools
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
95
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
96 Development has now moved to a dedicated GitHub repository:
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
97 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
98
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
99 For pushing a release to the test or main "Galaxy Tool Shed", use the following
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
100 Planemo commands (which requires you have set your Tool Shed access details in
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
101 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
102
17
557118c7e29e planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 3c6f0dca0e1318eecd1e07d177ffc5752b4f6c95
peterjc
parents: 16
diff changeset
103 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
104 ...
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
105
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
106 or::
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
107
17
557118c7e29e planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 3c6f0dca0e1318eecd1e07d177ffc5752b4f6c95
peterjc
parents: 16
diff changeset
108 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
109 ...
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
110
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
111 To just build and check the tar ball, use::
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
112
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
113 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira3/
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
114 ...
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
115 $ tar -tzf shed_upload.tar.gz
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
116 test-data/empty_file.dat
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
117 test-data/tvc_contigs.fasta
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
118 test-data/tvc_mini.fastq
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
119 tools/mira3/README.rst
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
120 tools/mira3/mira.py
16
f74bc0420db4 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/mira3/ commit 41e2a291e2e3925f834f18e48614e091e2df7643
peterjc
parents: 15
diff changeset
121 tools/mira3/mira.xml
12
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
122 tools/mira3/tool_dependencies.xml
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
123
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
124
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
125 Licence (MIT)
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
126 =============
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
127
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
128 Permission is hereby granted, free of charge, to any person obtaining a copy
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
129 of this software and associated documentation files (the "Software"), to deal
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
130 in the Software without restriction, including without limitation the rights
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
131 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
132 copies of the Software, and to permit persons to whom the Software is
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
133 furnished to do so, subject to the following conditions:
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
134
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
135 The above copyright notice and this permission notice shall be included in
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
136 all copies or substantial portions of the Software.
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
137
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
138 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
139 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
140 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
141 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
142 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
143 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
5b0af75dfe5a Uploaded v0.0.9, correct path in dependency installation; renamed folder
peterjc
parents:
diff changeset
144 THE SOFTWARE.