Mercurial > repos > peterjc > seq_primer_clip

annotate tools/primers/README.rst @ 4:c6bb189bf7c0 draft

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