Mercurial > repos > peterjc > get_orfs_or_cdss

comparison tools/get_orfs_or_cdss/README.rst @ 7:705a2e2df7fb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
author peterjc
date Thu, 30 Jul 2015 12:35:31 -0400
parents 64e67f172188
children 09a8be9247ca
comparison
equal deleted inserted replaced
6:64e67f172188 7:705a2e2df7fb
1 Galaxy tool to find ORFs or simple CDSs 1 Galaxy tool to find ORFs or simple CDSs
2 ======================================= 2 =======================================
3 3
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2011-2015 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 Biopython library functions) 8 This tool is a short Python script (using Biopython library functions)
9 to search nucleotide sequences for open reading frames (ORFs) or coding 9 to search nucleotide sequences for open reading frames (ORFs) or coding
29 Manual Installation 29 Manual Installation
30 =================== 30 ===================
31 31
32 There are just two files to install to use this tool from within Galaxy: 32 There are just two files to install to use this tool from within Galaxy:
33 33
34 * get_orfs_or_cdss.py (the Python script) 34 * ``get_orfs_or_cdss.py`` (the Python script)
35 * get_orfs_or_cdss.xml (the Galaxy tool definition) 35 * ``get_orfs_or_cdss.xml`` (the Galaxy tool definition)
36 36
37 The suggested location is in a dedicated tools/get_orfs_or_cdss folder. 37 The suggested location is in a dedicated ``tools/get_orfs_or_cdss`` folder.
38 38
39 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the 39 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
40 tool. One suggested location is in the filters section. Simply add the line:: 40 tool. One suggested location is in the filters section. Simply add the line::
41 41
42 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" /> 42 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" />
43 43
44 You will also need to install Biopython 1.54 or later. If you want to run 44 You will also need to install Biopython 1.65 or later (slightly older versions
45 the unit tests, include this line in tools_conf.xml.sample and the sample 45 should be fine, but will not have the latest NCBI genetic code tables).
46 FASTA files under the test-data directory. Then::
47 46
48 ./run_functional_tests.sh -id get_orfs_or_cdss 47 If you wish to run the unit tests, also move/copy the ``test-data/`` files
48 under Galaxy's ``test-data/`` folder. Then::
49
50 ./run_tests.sh -id get_orfs_or_cdss
49 51
50 That's it. 52 That's it.
51 53
52 54
53 History 55 History
66 - Use reStructuredText for this README file. 68 - Use reStructuredText for this README file.
67 - Adopt standard MIT License. 69 - Adopt standard MIT License.
68 - Updated citation information (Cock et al. 2013). 70 - Updated citation information (Cock et al. 2013).
69 - Renamed folder and adopted README.rst naming. 71 - Renamed folder and adopted README.rst naming.
70 v0.0.6 - Corrected automated dependency defintion. 72 v0.0.6 - Corrected automated dependency defintion.
73 v0.0.7 - Tool definition now embeds citation information.
74 v0.1.0 - Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
75 - Using ``optparse`` for the Python command line API (Eric Rasche).
76 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
77 v0.1.1 - Reorder XML elements (internal change only).
71 ======= ====================================================================== 78 ======= ======================================================================
72 79
73 80
74 Developers 81 Developers
75 ========== 82 ==========
78 http://bitbucket.org/peterjc/galaxy-central/src/tools 85 http://bitbucket.org/peterjc/galaxy-central/src/tools
79 86
80 Development has now moved to a dedicated GitHub repository: 87 Development has now moved to a dedicated GitHub repository:
81 https://github.com/peterjc/pico_galaxy/tree/master/tools 88 https://github.com/peterjc/pico_galaxy/tree/master/tools
82 89
83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 90 For pushing a release to the test or main "Galaxy Tool Shed", use the following
84 the following command from the Galaxy root folder:: 91 Planemo commands (which requires you have set your Tool Shed access details in
92 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
85 93
86 $ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/tool_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta 94 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
95 ...
87 96
88 Check this worked:: 97 or::
89 98
90 $ tar -tzf get_orfs_or_cdss.tar.gz 99 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
91 tools/get_orfs_or_cdss/README.rst 100 ...
92 tools/get_orfs_or_cdss/get_orfs_or_cdss.py 101
93 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml 102 To just build and check the tar ball, use::
94 tools/get_orfs_or_cdss/tool_dependencies.xml 103
95 test-data/get_orf_input.fasta 104 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
105 ...
106 $ tar -tzf shed_upload.tar.gz
107 test-data/Ssuis.fasta
108 test-data/get_orf_input.Suis_ORF.bed
96 test-data/get_orf_input.Suis_ORF.nuc.fasta 109 test-data/get_orf_input.Suis_ORF.nuc.fasta
97 test-data/get_orf_input.Suis_ORF.prot.fasta 110 test-data/get_orf_input.Suis_ORF.prot.fasta
111 test-data/get_orf_input.fasta
112 test-data/get_orf_input.t11_bed_out.bed
98 test-data/get_orf_input.t11_nuc_out.fasta 113 test-data/get_orf_input.t11_nuc_out.fasta
114 test-data/get_orf_input.t11_open_bed_out.bed
99 test-data/get_orf_input.t11_open_nuc_out.fasta 115 test-data/get_orf_input.t11_open_nuc_out.fasta
100 test-data/get_orf_input.t11_open_prot_out.fasta 116 test-data/get_orf_input.t11_open_prot_out.fasta
101 test-data/get_orf_input.t11_prot_out.fasta 117 test-data/get_orf_input.t11_prot_out.fasta
118 test-data/get_orf_input.t1_bed_out.bed
102 test-data/get_orf_input.t1_nuc_out.fasta 119 test-data/get_orf_input.t1_nuc_out.fasta
103 test-data/get_orf_input.t1_prot_out.fasta 120 test-data/get_orf_input.t1_prot_out.fasta
104 test-data/Ssuis.fasta 121 tools/get_orfs_or_cdss/get_orfs_or_cdss.py
122 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
123 tools/get_orfs_or_cdss/README.rst
124 tools/get_orfs_or_cdss/tool_dependencies.xml
105 125
106 126
107 Licence (MIT) 127 Licence (MIT)
108 ============= 128 =============
109 129