Mercurial > repos > peterjc > seq_primer_clip

annotate tools/primers/README.rst @ 3:f9ddb43ce28d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.10a, fixes Biopython dependency setup
author peterjc
date Fri, 13 Sep 2013 06:09:54 -0400
parents bd151574bbf3
children c6bb189bf7c0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
2 ===========================================================
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
3
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
6 See the licence text below (MIT licence).
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
7
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
8 This tool is a short Python script (using the Galaxy library functions and
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
9 Biopython). It is available from the Galaxy Tool Shed here:
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
10 http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
11
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
12
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
13 Automated Installation
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
14 ======================
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
15
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
16 This should be straightforward using the Galaxy Tool Shed, which should be
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
17 able to automatically install the dependency on Biopython, and then install
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
18 this tool and run its unit tests.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
19
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
20
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
21 Manual Installation
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
22 ===================
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
23
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
24 There are just two files to install:
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
25
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
26 * seq_primer_clip.py (the Python script)
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
27 * seq_primer_clip.xml (the Galaxy tool definition)
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
28
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
29 The suggested location is a new tools/primers folder. You will also need to
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
30 modify the tools_conf.xml file to tell Galaxy to offer the tool::
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
31
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
32 <tool file="primers/seq_primer_clip.xml" />
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
33
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
34 If you wish to run the unit tests, also add this to tools_conf.xml.sample
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
35 and move/copy the test-data files under Galaxy's test-data folder. Then::
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
36
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
37 $ ./run_functional_tests.sh -id seq_primer_clip
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
38
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
39 You will also need to install Biopython 1.54 or later. That's it.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
40
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
41
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
42 History
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
43 =======
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
44
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
45 ======= ======================================================================
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
46 Version Changes
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
47 ------- ----------------------------------------------------------------------
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
48 v0.0.1 - Initial version (not publicly released)
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
49 v0.0.2 - Sort primers by length (longest and therefore most specific first)
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
50 v0.0.3 - Consider missing bases at start/end of read as mismatches
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
51 v0.0.4 - Apply minimum length to sequences with no match too
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
52 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
53 v0.0.6 - Added some functional tests
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
54 v0.0.7 - Added error check for bad filename arguments
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
55 v0.0.8 - Record version of Python script when run from Galaxy.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
56 - Check for errors using Python script's return code.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
57 v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
58 v0.0.10 - Include links to Tool Shed in help text and this README file.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
59 - Use reStructuredText for this README file.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
60 - Adopted standard MIT licence.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
61 - Automated installation of Biopython dependency.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
62 ======= ======================================================================
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
63
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
64
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
65 Developers
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
66 ==========
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
67
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
68 This script and related tools are being developed on the following hg branch:
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
69 http://bitbucket.org/peterjc/galaxy-central/src/tools
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
70
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
71 This incorporates the previously used hg branch:
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
72 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
73
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
74 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
75 the following command from the Galaxy root folder::
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
76
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
77 $ tar -czf seq_primer_clip.tar.gz tools/primers/README.rst tools/primers/seq_primer_clip.* tools/primers/repository_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30*
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
78
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
79 Check this worked::
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
80
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
81 $ tar -tzf seq_primer_clip.tar.gz
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
82 tools/primers/README.rst
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
83 tools/primers/seq_primer_clip.xml
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
84 tools/primers/seq_primer_clip.py
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
85 tools/primers/repository_dependencies.xml
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
86 test-data/dop_primers.fasta
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
87 test-data/MID4_GLZRM4E04_rnd30.fasta
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
88 test-data/MID4_GLZRM4E04_rnd30.fastqsanger
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
89 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
90 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
91 test-data/MID4_GLZRM4E04_rnd30_fclip.sff
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
92 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
93 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
94 test-data/MID4_GLZRM4E04_rnd30_frclip.sff
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
95 test-data/MID4_GLZRM4E04_rnd30.sff
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
96
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
97
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
98 Licence (MIT)
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
99 =============
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
100
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
101 Permission is hereby granted, free of charge, to any person obtaining a copy
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
102 of this software and associated documentation files (the "Software"), to deal
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
103 in the Software without restriction, including without limitation the rights
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
104 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
105 copies of the Software, and to permit persons to whom the Software is
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
106 furnished to do so, subject to the following conditions:
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
107
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
108 The above copyright notice and this permission notice shall be included in
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
109 all copies or substantial portions of the Software.
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
110
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
111 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
112 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
113 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
114 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
115 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
116 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
bd151574bbf3 Uploaded v0.0.10, README.rst, MIT licence, biopython dependency
peterjc
parents:
diff changeset
117 THE SOFTWARE.