Mercurial > repos > peterjc > seq_primer_clip
comparison tools/seq_primer_clip/README.rst @ 4:9b074c1db68e draft
v0.0.14 galaxy_sequence_utils dependency etc
author | peterjc |
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date | Thu, 02 Feb 2017 11:52:37 -0500 |
parents | 708ce1e5ac94 |
children | 530c8d6fedd8 |
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1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads | 1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads |
2 =========================================================== | 2 =========================================================== |
3 | 3 |
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute | 4 This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
6 See the licence text below (MIT licence). | 6 See the licence text below (MIT licence). |
7 | 7 |
8 This tool is a short Python script (using the Galaxy library functions and | 8 This tool is a short Python script (using the Galaxy library functions and |
9 Biopython). It is available from the Galaxy Tool Shed here: | 9 Biopython). It is available from the Galaxy Tool Shed here: |
21 Manual Installation | 21 Manual Installation |
22 =================== | 22 =================== |
23 | 23 |
24 There are just two files to install: | 24 There are just two files to install: |
25 | 25 |
26 * seq_primer_clip.py (the Python script) | 26 * ``seq_primer_clip.py`` (the Python script) |
27 * seq_primer_clip.xml (the Galaxy tool definition) | 27 * ``seq_primer_clip.xml`` (the Galaxy tool definition) |
28 | 28 |
29 The suggested location is a new tools/seq_primer_clip folder. You will also | 29 The suggested location is a new ``tools/seq_primer_clip/`` folder. You will |
30 need to modify the tools_conf.xml file to tell Galaxy to offer the tool:: | 30 also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the |
31 tool:: | |
31 | 32 |
32 <tool file="seq_primer_clip/seq_primer_clip.xml" /> | 33 <tool file="seq_primer_clip/seq_primer_clip.xml" /> |
33 | 34 |
34 If you wish to run the unit tests, also add this to tools_conf.xml.sample | 35 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
35 and move/copy the test-data files under Galaxy's test-data folder. Then:: | 36 under Galaxy's ``test-data/`` folder. Then:: |
36 | 37 |
37 $ ./run_functional_tests.sh -id seq_primer_clip | 38 $ ./run_tests.sh -id seq_primer_clip |
38 | 39 |
39 You will also need to install Biopython 1.54 or later. That's it. | 40 You will also need to install Biopython 1.54 or later. That's it. |
40 | 41 |
41 | 42 |
42 History | 43 History |
60 - Adopted standard MIT licence. | 61 - Adopted standard MIT licence. |
61 - Automated installation of Biopython dependency. | 62 - Automated installation of Biopython dependency. |
62 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy | 63 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
63 - Renamed folder and adopted README.rst naming. | 64 - Renamed folder and adopted README.rst naming. |
64 v0.0.11 - Correct automated dependency definition. | 65 v0.0.11 - Correct automated dependency definition. |
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. | |
72 v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed). | |
73 - Explicit dependency on ``galaxy_sequence_utils``. | |
65 ======= ====================================================================== | 74 ======= ====================================================================== |
66 | 75 |
67 | 76 |
68 Developers | 77 Developers |
69 ========== | 78 ========== |
73 http://bitbucket.org/peterjc/galaxy-central/src/tools | 82 http://bitbucket.org/peterjc/galaxy-central/src/tools |
74 | 83 |
75 Development has now moved to a dedicated GitHub repository: | 84 Development has now moved to a dedicated GitHub repository: |
76 https://github.com/peterjc/pico_galaxy | 85 https://github.com/peterjc/pico_galaxy |
77 | 86 |
78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
79 the following command from the Galaxy root folder:: | |
80 | 87 |
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* | 88 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
89 Planemo commands (which requires you have set your Tool Shed access details in | |
90 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
82 | 91 |
83 Check this worked:: | 92 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ |
93 ... | |
84 | 94 |
85 $ tar -tzf seq_primer_clip.tar.gz | 95 or:: |
86 tools/seq_primer_clip/README.rst | 96 |
87 tools/seq_primer_clip/seq_primer_clip.xml | 97 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ |
88 tools/seq_primer_clip/seq_primer_clip.py | 98 ... |
89 tools/seq_primer_clip/tool_dependencies.xml | 99 |
90 test-data/dop_primers.fasta | 100 To just build and check the tar ball, use:: |
101 | |
102 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_primer_clip/ | |
103 ... | |
104 $ tar -tzf shed_upload.tar.gz | |
91 test-data/MID4_GLZRM4E04_rnd30.fasta | 105 test-data/MID4_GLZRM4E04_rnd30.fasta |
92 test-data/MID4_GLZRM4E04_rnd30.fastqsanger | 106 test-data/MID4_GLZRM4E04_rnd30.fastqsanger |
93 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta | 107 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta |
94 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger | 108 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
95 test-data/MID4_GLZRM4E04_rnd30_fclip.sff | 109 test-data/MID4_GLZRM4E04_rnd30_fclip.sff |
96 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta | 110 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta |
97 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger | 111 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger |
98 test-data/MID4_GLZRM4E04_rnd30_frclip.sff | 112 test-data/MID4_GLZRM4E04_rnd30_frclip.sff |
99 test-data/MID4_GLZRM4E04_rnd30.sff | 113 test-data/MID4_GLZRM4E04_rnd30.sff |
114 test-data/dop_primers.fasta | |
115 tools/seq_primer_clip/README.rst | |
116 tools/seq_primer_clip/seq_primer_clip.py | |
117 tools/seq_primer_clip/seq_primer_clip.xml | |
118 tools/seq_primer_clip/tool_dependencies.xml | |
100 | 119 |
101 | 120 |
102 Licence (MIT) | 121 Licence (MIT) |
103 ============= | 122 ============= |
104 | 123 |