Mercurial > repos > devteam > blast_datatypes
annotate 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 |
|---|---|
| date | Wed, 20 Mar 2013 10:39:27 -0400 |
| parents | f9a7783ed7b6 |
| children |
| rev | line source |
|---|---|
| 3 | 1 Galaxy datatypes for NCBI BLAST+ suite |
| 2 ====================================== | |
| 3 | |
|
5
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
4 These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton |
| 3 | 5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
|
5
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
6 Contributions/revisions copyright 2012 Edward Kirton. All rights reserved. |
|
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
7 Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved. |
|
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
8 |
| 3 | 9 See the licence text below. |
| 10 | |
| 11 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 | |
| 13 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the | |
| 14 wrappers). My thanks to Dannon Baker from the Galaxy development team for his | |
| 15 assistance with this. | |
| 16 | |
| 17 | |
| 18 History | |
| 19 ======= | |
| 20 | |
| 21 These versions numbers match those for 'ncbi_blast_plus', but are not used | |
| 22 explicitly in the datatypes themselves. | |
| 23 | |
| 24 v0.0.11 - Final revision as part of the Galaxy main repository, and the | |
| 25 first release via the Tool Shed | |
| 26 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes | |
| 4 | 27 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases |
| 28 (based on work by Edward Kirton) | |
|
5
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
29 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional |
|
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
30 BLAST database files (contribution from Nicola Soranzo) |
| 3 | 31 |
| 32 | |
| 33 Installation | |
| 34 ============ | |
| 35 | |
| 36 Doing this automatically via the Galaxy Tool Shed is probably simplest. | |
| 37 | |
| 38 | |
| 39 Manual Installation | |
| 40 =================== | |
| 41 | |
| 42 Normally you would install this via the Galaxy ToolShed, which would move | |
| 43 the provided blast.py file into a suitable location and process the | |
| 44 datatypes_conf.xml entry to be combined with your local configuration. | |
| 45 | |
| 46 However, if you really want to this should work for a manual install. Add | |
| 4 | 47 the following lines to the datatypes_conf.xml file in the Galaxy main folder: |
| 3 | 48 |
| 49 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> | |
| 4 | 50 <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/> |
| 51 <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/> | |
| 52 | |
| 53 and later in the sniffer section: | |
| 54 | |
| 55 <sniffer type="galaxy.datatypes.blast:BlastXml"/> | |
| 3 | 56 |
| 57 Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking | |
| 58 the blast.py file provided in this tar-ball. Finally add 'import blast' near | |
| 59 the start of file lib/galaxy/datatypes/registry.py (after the other import | |
| 60 lines). | |
| 61 | |
| 62 | |
| 63 Developers | |
| 64 ========== | |
| 65 | |
| 66 BLAST+ datatypes and wrappers, and other tools are being developed on the | |
| 67 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 68 | |
|
5
b3a3ba0c1d47
Uploaded v0.0.15 which updates the BLAST database definitions.
peterjc
parents:
4
diff
changeset
|
69 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use |
| 3 | 70 the following command from the Galaxy tools/ncbi_blast_plus folder: |
| 71 | |
| 72 $ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py | |
| 73 | |
| 74 Check this worked: | |
| 75 | |
| 76 $ tar -tzf blast_datatypes.tar.gz | |
| 77 blast_datatypes.txt | |
| 78 datatypes_conf.xml | |
| 79 blast.py | |
| 80 | |
| 81 Note that the placement of these three files under tools/ncbi_blast_plus is | |
| 82 arbitrary - this just puts them next to the tool wrappers which use them. | |
| 83 | |
| 84 For development, rather than having a local ToolShed running, I currently | |
| 85 use a symlink from lib/galaxy/datatypes/blast.py to the actual file | |
| 86 tools/ncbi_blast_plus/blast.py as described above. | |
| 87 | |
| 88 | |
| 89 Licence (MIT/BSD style) | |
| 90 ======================= | |
| 91 | |
| 92 Permission to use, copy, modify, and distribute this software and its | |
| 93 documentation with or without modifications and for any purpose and | |
| 94 without fee is hereby granted, provided that any copyright notices | |
| 95 appear in all copies and that both those copyright notices and this | |
| 96 permission notice appear in supporting documentation, and that the | |
| 97 names of the contributors or copyright holders not be used in | |
| 98 advertising or publicity pertaining to distribution of the software | |
| 99 without specific prior permission. | |
| 100 | |
| 101 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 102 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 103 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 104 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 105 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 106 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 107 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 108 OR PERFORMANCE OF THIS SOFTWARE. | |
| 109 | |
| 110 NOTE: This is the licence for the Galaxy BLAST datatypes only. BLAST+ | |
| 111 and associated data files are available and licenced separately. |