Mercurial > repos > devteam > blast_datatypes
comparison blast_datatypes.txt @ 4:f9a7783ed7b6 draft
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). |