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