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Uploaded v0.0.19, adds blastdbp and pssm-asn1 datatypes.
author peterjc
date Wed, 26 Nov 2014 06:55:48 -0500
parents de11e1a921c4
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1 Galaxy datatypes for NCBI BLAST+ suite 1 Galaxy datatypes for NCBI BLAST+ suite
2 ====================================== 2 ======================================
3 3
4 These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton 4 These Galaxy datatypes are copyright 2010-2014 by Peter Cock (The James Hutton
5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 Institute, UK) and additional contributors including Edward Kirton, Nicola
6 Contributions/revisions copyright 2012 Edward Kirton. All rights reserved. 6 Soranzo, and Bjoern Gruening.
7 Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
8 7
9 See the licence text below. 8 See the licence text below.
10 9
11 Note that these files (and the associated BLAST+ wrappers) were originally 10 Note that these files (and the associated BLAST+ wrappers) were originally
12 distributed as part of the main Galaxy repository, but as of August 2012 moved 11 distributed as part of the main Galaxy repository, but as of August 2012 moved
27 ======= ====================================================================== 26 ======= ======================================================================
28 Version Changes 27 Version Changes
29 ------- ---------------------------------------------------------------------- 28 ------- ----------------------------------------------------------------------
30 v0.0.11 - Final revision as part of the Galaxy main repository, and the 29 v0.0.11 - Final revision as part of the Galaxy main repository, and the
31 first release via the Tool Shed 30 first release via the Tool Shed
32 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes 31 v0.0.13 - Uses ``blast.py`` instead of ``xml.py`` to define the datatypes
33 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases 32 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
34 (based on work by Edward Kirton) 33 (``blastdbp`` and ``blastdbn``, based on work by Edward Kirton)
35 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional 34 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
36 BLAST database files (contribution from Nicola Soranzo) 35 BLAST database files (contribution from Nicola Soranzo)
37 v0.0.16 - Adopt standard MIT License. 36 v0.0.16 - Adopt standard MIT License.
38 - Use reStructuredText for this README file. 37 - Use reStructuredText for this README file.
39 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast 38 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
40 - Nucleotide database definition aware of MegaBLAST index superheader 39 - Nucleotide database definition aware of MegaBLAST index superheader
41 v0.0.17 - Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes 40 v0.0.17 - Add ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` sub-datatypes
41 (contribution from Nicola Soranzo)
42 v0.0.18 - Add retries to BLAST XML merge code. 42 v0.0.18 - Add retries to BLAST XML merge code.
43 - Modify display_data method to allow unit tests to function. 43 - Modify display_data method to allow unit tests to function.
44 v0.0.19 - Add ``blastdbp`` datatype for BLAST protein domain databases, for use
45 with makeprofiledb and rpsblast (contribution from Bjoern Gruening).
46 - Add ``pssm-asn1`` datatype for Position Specific Scoring Matrices
47 (PSSMs) stored in NCBI's "scoremat" ASN.1 format (usually named
48 as *.smp), used as input files for makeprofiledb.
44 ======= ====================================================================== 49 ======= ======================================================================
45 50
46 51
47 Installation 52 Installation
48 ============ 53 ============
52 57
53 Manual Installation 58 Manual Installation
54 =================== 59 ===================
55 60
56 Normally you would install this via the Galaxy ToolShed, which would move 61 Normally you would install this via the Galaxy ToolShed, which would move
57 the provided blast.py file into a suitable location and process the 62 the provided ``blast.py`` file into a suitable location and process the
58 datatypes_conf.xml entry to be combined with your local configuration. 63 ``datatypes_conf.xml`` entries to be combined with your local configuration.
59 64
60 However, if you really want to this should work for a manual install. Add 65 However, if you really want to this should work for a manual install. First
61 the following lines to the datatypes_conf.xml file in the Galaxy main folder:: 66 update the ``datatypes_conf.xml`` file in the Galaxy main folder by inserting
67 the contents of the ``<registration>`` and ``<sniffers>`` sections from the
68 small ``datatypes_conf.xml`` file provided in the tar-ball.
69
70 For the ``<registration>`` section you would add several ``<datatype ... />``
71 lines, one per new datatype::
62 72
63 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> 73 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
64 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/> 74 ...
65 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
66 75
67 and later in the sniffer section:: 76 Similarly, some of the new dataypes have ``<sniffer ... />`` lines used to
77 automatically recognise the datatype when uploaded into Galaxy::
68 78
69 <sniffer type="galaxy.datatypes.blast:BlastXml"/> 79 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
80 ...
70 81
71 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking 82 Also create the file ``lib/galaxy/datatypes/blast.py`` by moving, copying or linking
72 the blast.py file provided in this tar-ball. Finally add 'import blast' near 83 the ``blast.py`` file provided in this tar-ball. Finally add ``import blast`` near
73 the start of file lib/galaxy/datatypes/registry.py (after the other import 84 the start of file ``lib/galaxy/datatypes/registry.py`` (after the other import
74 lines). 85 lines).
75 86
76 87
77 Bug Reports 88 Bug Reports
78 =========== 89 ===========
82 93
83 94
84 Developers 95 Developers
85 ========== 96 ==========
86 97
87 BLAST+ datatypes and wrappers, and other tools were originally developed on the 98 These BLAST+ datatypes and associated tools were originally developed on the
88 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools 99 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
89 100
90 As of July 2013, development is continuing on a dedicated GitHub repository: 101 As of July 2013, development is continuing on a dedicated GitHub repository:
91 https://github.com/peterjc/galaxy_blast 102 https://github.com/peterjc/galaxy_blast
92 103
93 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use 104 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
94 the following command from the blast_datatypes folder:: 105 the following command from the ``blast_datatypes`` folder::
95 106
96 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py 107 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
97 108
98 Check this worked:: 109 Check this worked::
99 110
101 README.rst 112 README.rst
102 datatypes_conf.xml 113 datatypes_conf.xml
103 blast.py 114 blast.py
104 115
105 For development, rather than having a local ToolShed running, I currently 116 For development, rather than having a local ToolShed running, I currently
106 use a symlink from lib/galaxy/datatypes/blast.py to the actual file as 117 use a symlink from ``lib/galaxy/datatypes/blast.py`` to the actual file as
107 described above. 118 described above.
108 119
109 120
110 Licence (MIT) 121 Licence (MIT)
111 ============= 122 =============