Mercurial > repos > peterjc > seq_primer_clip
annotate tools/seq_primer_clip/README.rst @ 6:b9dc7c967ee6 draft default tip
v0.0.16 Python 3 compatible print function
author | peterjc |
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date | Tue, 16 May 2017 09:36:50 -0400 |
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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 |
4 | 4 This tool is copyright 2011-2017 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 |
4 | 26 * ``seq_primer_clip.py`` (the Python script) |
27 * ``seq_primer_clip.xml`` (the Galaxy tool definition) | |
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28 |
4 | 29 The suggested location is a new ``tools/seq_primer_clip/`` folder. You will |
30 also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the | |
31 tool:: | |
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32 |
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33 <tool file="seq_primer_clip/seq_primer_clip.xml" /> |
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34 |
4 | 35 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
36 under Galaxy's ``test-data/`` folder. Then:: | |
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37 |
4 | 38 $ ./run_tests.sh -id seq_primer_clip |
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39 |
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40 You will also need to install Biopython 1.54 or later. That's it. |
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41 |
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42 |
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43 History |
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44 ======= |
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45 |
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46 ======= ====================================================================== |
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47 Version Changes |
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48 ------- ---------------------------------------------------------------------- |
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49 v0.0.1 - Initial version (not publicly released) |
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50 v0.0.2 - Sort primers by length (longest and therefore most specific first) |
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51 v0.0.3 - Consider missing bases at start/end of read as mismatches |
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52 v0.0.4 - Apply minimum length to sequences with no match too |
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53 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes |
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54 v0.0.6 - Added some functional tests |
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55 v0.0.7 - Added error check for bad filename arguments |
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56 v0.0.8 - Record version of Python script when run from Galaxy. |
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57 - Check for errors using Python script's return code. |
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58 v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation. |
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59 v0.0.10 - Include links to Tool Shed in help text and this README file. |
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60 - Use reStructuredText for this README file. |
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61 - Adopted standard MIT licence. |
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62 - Automated installation of Biopython dependency. |
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63 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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64 - Renamed folder and adopted README.rst naming. |
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65 v0.0.11 - Correct automated dependency definition. |
4 | 66 v0.0.12 - Simplified XML to apply input format to output data. |
67 - Tool definition now embeds citation information. | |
68 v0.0.13 - Use ``format_source=...`` tag. | |
69 - Reorder XML elements (internal change only). | |
70 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
71 - Fixed input file help text. | |
5 | 72 v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. |
4 | 73 - Explicit dependency on ``galaxy_sequence_utils``. |
5 | 74 v0.0.15 - Use ``<command detect_errors="aggressive">`` (internal change only). |
75 - Single quote command line arguments (internal change only) | |
6 | 76 v0.0.16 - Python 3 compatible print function. |
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77 ======= ====================================================================== |
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78 |
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79 |
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80 Developers |
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81 ========== |
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82 |
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83 This script and related tools were initially developed on the following hg branches: |
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84 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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85 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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86 |
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87 Development has now moved to a dedicated GitHub repository: |
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88 https://github.com/peterjc/pico_galaxy |
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89 |
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90 |
4 | 91 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
92 Planemo commands (which requires you have set your Tool Shed access details in | |
93 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
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94 |
5 | 95 $ planemo shed_update -t testtoolshed --check_diff tools/seq_primer_clip/ |
4 | 96 ... |
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97 |
4 | 98 or:: |
99 | |
5 | 100 $ planemo shed_update -t toolshed --check_diff tools/seq_primer_clip/ |
4 | 101 ... |
102 | |
103 To just build and check the tar ball, use:: | |
104 | |
5 | 105 $ planemo shed_upload --tar_only tools/seq_primer_clip/ |
4 | 106 ... |
107 $ tar -tzf shed_upload.tar.gz | |
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108 test-data/MID4_GLZRM4E04_rnd30.fasta |
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109 test-data/MID4_GLZRM4E04_rnd30.fastqsanger |
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110 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta |
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111 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
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112 test-data/MID4_GLZRM4E04_rnd30_fclip.sff |
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113 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta |
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114 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger |
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115 test-data/MID4_GLZRM4E04_rnd30_frclip.sff |
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116 test-data/MID4_GLZRM4E04_rnd30.sff |
4 | 117 test-data/dop_primers.fasta |
118 tools/seq_primer_clip/README.rst | |
119 tools/seq_primer_clip/seq_primer_clip.py | |
120 tools/seq_primer_clip/seq_primer_clip.xml | |
121 tools/seq_primer_clip/tool_dependencies.xml | |
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122 |
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123 |
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124 Licence (MIT) |
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125 ============= |
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126 |
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127 Permission is hereby granted, free of charge, to any person obtaining a copy |
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128 of this software and associated documentation files (the "Software"), to deal |
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129 in the Software without restriction, including without limitation the rights |
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130 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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131 copies of the Software, and to permit persons to whom the Software is |
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132 furnished to do so, subject to the following conditions: |
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133 |
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134 The above copyright notice and this permission notice shall be included in |
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135 all copies or substantial portions of the Software. |
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136 |
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137 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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138 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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139 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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140 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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141 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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142 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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143 THE SOFTWARE. |