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Uploaded v0.0.2
author peterjc
date Tue, 04 Nov 2014 07:15:50 -0500
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1 Galaxy wrapper for samtools bam2fq
2 ====================================
3
4 This wrapper is copyright 2014 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below.
7
8 This is a wrapper for part of the command line samtools suite.
9
10 This wrapper is available from the Galaxy Tool Shed at:
11 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
12
13
14 Automated Installation
15 ======================
16
17 This should be straightforward, Galaxy should automatically download and install
18 samtools if required.
19
20
21 Manual Installation
22 ===================
23
24 This expects samtools to be on the $PATH, and was tested using v0.1.19.
25
26 To install the wrapper copy or move the following files under the Galaxy tools
27 folder, e.g. in a ``tools/samtools_bam2fq`` folder:
28
29 * ``samtools_bam2fq.xml`` (the Galaxy tool definition)
30 * ``README.rst`` (this file)
31
32 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
33 the tool. Just add the line, perhaps under the NGS tools section::
34
35 <tool file="samtools_bam2fq/samtools_bam2fq.xml" />
36
37 If you wish to run the unit tests, also move/copy the ``test-data/`` files
38 under Galaxy's ``test-data/`` folder. Then::
39
40 $ ./run_tests.sh -id samtools_bam2fq
41
42 That's it.
43
44
45 History
46 =======
47
48 ======= ======================================================================
49 Version Changes
50 ------- ----------------------------------------------------------------------
51 v0.0.1 - Initial public release, tested with samtools v1.1.
52 v0.0.2 - Defaults to pair-aware mode which requires pre-sorting by read name.
53 ======= ======================================================================
54
55
56 Developers
57 ==========
58
59 Development is on this GitHub repository:
60 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq
61
62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
63 the following command from the Galaxy root folder::
64
65 $ tar -czf samtools_bam2fq.tar.gz tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/tool_dependencies.xml test-data/sam_spec_padded.bam test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq test-data/sam_spec_padded.bam2fq_no_suf.fastq test-data/sam_spec_padded.bam2fq_singles.fastq test-data/sam_spec_padded.bam2fq_pairs.fastq
66
67 Check this worked::
68
69 $ tar -tzf samtools_bam2fq.tar.gz
70 tools/samtools_bam2fq/README.rst
71 tools/samtools_bam2fq/samtools_bam2fq.xml
72 tools/samtools_bam2fq/tool_dependencies.xml
73 test-data/sam_spec_padded.bam
74 test-data/sam_spec_padded.sam
75 test-data/sam_spec_padded.depad.bam
76 test-data/sam_spec_padded.bam2fq.fastq
77 test-data/sam_spec_padded.bam2fq_no_suf.fastq
78 test-data/sam_spec_padded.bam2fq_singles.fastq
79 test-data/sam_spec_padded.bam2fq_pairs.fastq
80
81
82 Licence (MIT)
83 =============
84
85 Permission is hereby granted, free of charge, to any person obtaining a copy
86 of this software and associated documentation files (the "Software"), to deal
87 in the Software without restriction, including without limitation the rights
88 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
89 copies of the Software, and to permit persons to whom the Software is
90 furnished to do so, subject to the following conditions:
91
92 The above copyright notice and this permission notice shall be included in
93 all copies or substantial portions of the Software.
94
95 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
96 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
97 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
98 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
99 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
100 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
101 THE SOFTWARE.
102
103 NOTE: This is the licence for the Galaxy Wrapper only.
104 samtools is available and licenced separately.