Mercurial > repos > peterjc > seq_primer_clip
annotate tools/seq_primer_clip/README.rst @ 3:708ce1e5ac94 draft
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author | peterjc |
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date | Thu, 21 Nov 2013 10:47:23 -0500 |
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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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7 |
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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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11 |
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12 |
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13 Automated Installation |
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14 ====================== |
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15 |
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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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19 |
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20 |
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21 Manual Installation |
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22 =================== |
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23 |
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24 There are just two files to install: |
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25 |
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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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28 |
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29 The suggested location is a new tools/seq_primer_clip folder. You will also |
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30 need to modify the tools_conf.xml file to tell Galaxy to offer the tool:: |
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31 |
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32 <tool file="seq_primer_clip/seq_primer_clip.xml" /> |
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33 |
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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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36 |
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37 $ ./run_functional_tests.sh -id seq_primer_clip |
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38 |
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39 You will also need to install Biopython 1.54 or later. That's it. |
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40 |
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41 |
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42 History |
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43 ======= |
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44 |
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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 - Renamed folder and adopted README.rst naming. |
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64 v0.0.11 - Correct automated dependency definition. |
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65 ======= ====================================================================== |
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66 |
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67 |
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68 Developers |
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69 ========== |
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70 |
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71 This script and related tools were initially developed on the following hg branches: |
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72 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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73 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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74 |
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75 Development has now moved to a dedicated GitHub repository: |
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76 https://github.com/peterjc/pico_galaxy |
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77 |
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78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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79 the following command from the Galaxy root folder:: |
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80 |
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81 $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/tool_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* |
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82 |
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83 Check this worked:: |
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84 |
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85 $ tar -tzf seq_primer_clip.tar.gz |
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86 tools/seq_primer_clip/README.rst |
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87 tools/seq_primer_clip/seq_primer_clip.xml |
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88 tools/seq_primer_clip/seq_primer_clip.py |
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89 tools/seq_primer_clip/tool_dependencies.xml |
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90 test-data/dop_primers.fasta |
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91 test-data/MID4_GLZRM4E04_rnd30.fasta |
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92 test-data/MID4_GLZRM4E04_rnd30.fastqsanger |
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93 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta |
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94 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
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95 test-data/MID4_GLZRM4E04_rnd30_fclip.sff |
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96 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta |
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97 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger |
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98 test-data/MID4_GLZRM4E04_rnd30_frclip.sff |
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99 test-data/MID4_GLZRM4E04_rnd30.sff |
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100 |
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101 |
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102 Licence (MIT) |
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103 ============= |
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104 |
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105 Permission is hereby granted, free of charge, to any person obtaining a copy |
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106 of this software and associated documentation files (the "Software"), to deal |
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107 in the Software without restriction, including without limitation the rights |
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108 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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109 copies of the Software, and to permit persons to whom the Software is |
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110 furnished to do so, subject to the following conditions: |
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111 |
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112 The above copyright notice and this permission notice shall be included in |
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113 all copies or substantial portions of the Software. |
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114 |
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115 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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116 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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117 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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118 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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119 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
ee5acea162a7
Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency
peterjc
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120 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
ee5acea162a7
Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency
peterjc
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121 THE SOFTWARE. |