Mercurial > repos > devteam > blast_datatypes
comparison README.rst @ 9:2bda64d39931 draft
Uploaded v0.0.19, adds blastdbp and pssm-asn1 datatypes.
author | peterjc |
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date | Wed, 26 Nov 2014 06:55:48 -0500 |
parents | de11e1a921c4 |
children | 5482a8cd0f36 |
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8:de11e1a921c4 | 9:2bda64d39931 |
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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 ============= |