Mercurial > repos > devteam > ncbi_blast_plus
comparison ncbi_blast_plus.txt @ 2:ab1a8640f817 draft
Uploaded v0.0.12 again, without extra path
author | peterjc |
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date | Thu, 23 Aug 2012 07:32:06 -0400 |
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1 Galaxy wrappers for NCBI BLAST+ suite | |
2 ===================================== | |
3 | |
4 These wrappers are copyright 2010-2012 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), | |
9 and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall). | |
10 | |
11 Note that these wrappers were originally distributed as part of the main | |
12 Galaxy repository, but as of August 2012 moved to the Galaxy Tool Shed. | |
13 My thanks to Dannon Baker from the Galaxy development team for this assistance | |
14 with this. | |
15 | |
16 | |
17 Manual Installation | |
18 =================== | |
19 | |
20 For those not using Galaxy's automated installation from the Tool Shed, put | |
21 the XML and Python files under tools/ncbi_blast_plus and add the XML files | |
22 to your tool_conf.xml as normal. | |
23 | |
24 You must tell Galaxy about any system level BLAST databases using configuration | |
25 files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein | |
26 databases like NR). | |
27 | |
28 You will also need to install the 'blast_datatypes' from the Tool Shed. This | |
29 defines the BLAST XML file format ('blastxml'). | |
30 | |
31 | |
32 History | |
33 ======= | |
34 | |
35 v0.0.11 - Final revision as part of the Galaxy main repository, and the | |
36 first release via the Tool Shed | |
37 v0.0.12 - Implements genetic code option for translation searches. | |
38 - Changes <parallelism> to 1000 sequences at a time (to cope with | |
39 very large sets of queries where BLAST+ can become memory hungry) | |
40 - Include warning that BLAST+ with subject FASTA gives pairwise | |
41 e-values | |
42 | |
43 | |
44 Developers | |
45 ========== | |
46 | |
47 This script and related tools are being developed on the following hg branch: | |
48 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
49 | |
50 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use | |
51 the following command from the Galaxy tools/ncbi_blast_plus folder: | |
52 | |
53 $ ./make_ncbi_blast_plus.sh | |
54 | |
55 This similifies ensuring a consistent set of files is bundled each time, | |
56 including all the relevant test files. | |
57 | |
58 | |
59 Licence (MIT/BSD style) | |
60 ======================= | |
61 | |
62 Permission to use, copy, modify, and distribute this software and its | |
63 documentation with or without modifications and for any purpose and | |
64 without fee is hereby granted, provided that any copyright notices | |
65 appear in all copies and that both those copyright notices and this | |
66 permission notice appear in supporting documentation, and that the | |
67 names of the contributors or copyright holders not be used in | |
68 advertising or publicity pertaining to distribution of the software | |
69 without specific prior permission. | |
70 | |
71 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
72 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
73 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
74 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
75 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
76 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
77 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
78 OR PERFORMANCE OF THIS SOFTWARE. | |
79 | |
80 NOTE: This is the licence for the Galaxy Wrapper only. BLAST+ and | |
81 associated data files are available and licenced separately. |