Mercurial > repos > devteam > blast_datatypes
view blast_datatypes.txt @ 5:b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
Fixes a MetadataElement bug and includes more of the optional
BLAST database files (contribution from Nicola Soranzo).
author | peterjc |
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date | Wed, 20 Mar 2013 10:39:27 -0400 |
parents | f9a7783ed7b6 |
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Galaxy datatypes for NCBI BLAST+ suite ====================================== These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. Contributions/revisions copyright 2012 Edward Kirton. All rights reserved. Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved. See the licence text below. Note that these files (and the associated BLAST+ wrappers) were originally distributed as part of the main Galaxy repository, but as of August 2012 moved to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the wrappers). My thanks to Dannon Baker from the Galaxy development team for his assistance with this. History ======= These versions numbers match those for 'ncbi_blast_plus', but are not used explicitly in the datatypes themselves. v0.0.11 - Final revision as part of the Galaxy main repository, and the first release via the Tool Shed v0.0.13 - Uses blast.py instead of xml.py to define the datatypes v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases (based on work by Edward Kirton) v0.0.15 - Fixes a MetadataElement bug and includes more of the optional BLAST database files (contribution from Nicola Soranzo) Installation ============ Doing this automatically via the Galaxy Tool Shed is probably simplest. Manual Installation =================== Normally you would install this via the Galaxy ToolShed, which would move the provided blast.py file into a suitable location and process the datatypes_conf.xml entry to be combined with your local configuration. However, if you really want to this should work for a manual install. Add the following lines to the datatypes_conf.xml file in the Galaxy main folder: <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/> <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/> and later in the sniffer section: <sniffer type="galaxy.datatypes.blast:BlastXml"/> Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking the blast.py file provided in this tar-ball. Finally add 'import blast' near the start of file lib/galaxy/datatypes/registry.py (after the other import lines). Developers ========== BLAST+ datatypes and wrappers, and other tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use the following command from the Galaxy tools/ncbi_blast_plus folder: $ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py Check this worked: $ tar -tzf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py Note that the placement of these three files under tools/ncbi_blast_plus is arbitrary - this just puts them next to the tool wrappers which use them. For development, rather than having a local ToolShed running, I currently use a symlink from lib/galaxy/datatypes/blast.py to the actual file tools/ncbi_blast_plus/blast.py as described above. Licence (MIT/BSD style) ======================= Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. NOTE: This is the licence for the Galaxy BLAST datatypes only. BLAST+ and associated data files are available and licenced separately.