comparison tools/seq_primer_clip/README.rst @ 4:9b074c1db68e draft

v0.0.14 galaxy_sequence_utils dependency etc
author peterjc
date Thu, 02 Feb 2017 11:52:37 -0500
parents 708ce1e5ac94
children 530c8d6fedd8
comparison
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3:708ce1e5ac94 4:9b074c1db68e
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