Mercurial > repos > devteam > blast_datatypes

comparison blast_datatypes.txt @ 4:f9a7783ed7b6

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Uploaded v0.0.14 adding BLAST database support. See also the matching update for the NCBI BLAST+ wrappers which use these new definitions. This update included work by Edward Kirton.
author peterjc
date Fri, 09 Nov 2012 06:50:05 -0500
parents 6ef523b390e0
children b3a3ba0c1d47
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3:6ef523b390e0 4:f9a7783ed7b6
19 explicitly in the datatypes themselves. 19 explicitly in the datatypes themselves.
20 20
21 v0.0.11 - Final revision as part of the Galaxy main repository, and the 21 v0.0.11 - Final revision as part of the Galaxy main repository, and the
22 first release via the Tool Shed 22 first release via the Tool Shed
23 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes 23 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
24 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
25 (based on work by Edward Kirton)
24 26
25 27
26 Installation 28 Installation
27 ============ 29 ============
28 30
35 Normally you would install this via the Galaxy ToolShed, which would move 37 Normally you would install this via the Galaxy ToolShed, which would move
36 the provided blast.py file into a suitable location and process the 38 the provided blast.py file into a suitable location and process the
37 datatypes_conf.xml entry to be combined with your local configuration. 39 datatypes_conf.xml entry to be combined with your local configuration.
38 40
39 However, if you really want to this should work for a manual install. Add 41 However, if you really want to this should work for a manual install. Add
40 the following line to the datatypes_conf.xml file in the Galaxy main folder: 42 the following lines to the datatypes_conf.xml file in the Galaxy main folder:
41 43
42 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> 44 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
45 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
46 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>
47
48 and later in the sniffer section:
49
50 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
43 51
44 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking 52 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
45 the blast.py file provided in this tar-ball. Finally add 'import blast' near 53 the blast.py file provided in this tar-ball. Finally add 'import blast' near
46 the start of file lib/galaxy/datatypes/registry.py (after the other import 54 the start of file lib/galaxy/datatypes/registry.py (after the other import
47 lines). 55 lines).