Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blast_plus.txt @ 9:9dabbfd73c8a draft
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
Also includes other minor improvements.
author | peterjc |
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date | Thu, 25 Apr 2013 09:38:37 -0400 |
parents | 1f546099212f |
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8:1f546099212f | 9:9dabbfd73c8a |
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4 These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute | 4 These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
6 See the licence text below. | 6 See the licence text below. |
7 | 7 |
8 Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), | 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). | 9 and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). |
10 | 10 |
11 Note that these wrappers (and the associated datetypes) were originally | 11 Note that these wrappers (and the associated datatypes) were originally |
12 distributed as part of the main Galaxy repository, but as of August 2012 | 12 distributed as part of the main Galaxy repository, but as of August 2012 |
13 moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). | 13 moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). |
14 My thanks to Dannon Baker from the Galaxy development team for his assistance | 14 My thanks to Dannon Baker from the Galaxy development team for his assistance |
15 with this. | 15 with this. |
16 | 16 |
23 ('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and | 23 ('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and |
24 'blastdbn'). | 24 'blastdbn'). |
25 | 25 |
26 You must tell Galaxy about any system level BLAST databases using configuration | 26 You must tell Galaxy about any system level BLAST databases using configuration |
27 files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein | 27 files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein |
28 databases like NR), located in the tool-data folder. Sample fils are included | 28 databases like NR), and blastdb_d.loc (protein domain databases like CDD or |
29 which explain the tab based format to use. | 29 SMART) which are located in the tool-data/ folder. Sample files are included |
30 which explain the tab-based format to use. | |
31 | |
32 You can download the NCBI provided databases as tar-balls from here: | |
33 ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) | |
34 ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) | |
30 | 35 |
31 | 36 |
32 Manual Installation | 37 Manual Installation |
33 =================== | 38 =================== |
34 | 39 |
35 For those not using Galaxy's automated installation from the Tool Shed, put | 40 For those not using Galaxy's automated installation from the Tool Shed, put |
36 the XML and Python files under tools/ncbi_blast_plus and add the XML files | 41 the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML |
37 to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample | 42 files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample |
38 in order to run the unit tests). For example, use: | 43 in order to run the unit tests). For example, use: |
39 | 44 |
40 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> | 45 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> |
41 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> | 46 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> |
42 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> | 47 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> |
44 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> | 49 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> |
45 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> | 50 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> |
46 <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> | 51 <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> |
47 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> | 52 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> |
48 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> | 53 <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> |
54 <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> | |
55 <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> | |
49 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> | 56 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> |
50 </section> | 57 </section> |
51 | 58 |
52 You will also need to install 'blast_datatypes' from the Tool Shed. This | 59 You will also need to install 'blast_datatypes' from the Tool Shed. This |
53 defines the BLAST XML file format ('blastxml') and protein and nucleotide | 60 defines the BLAST XML file format ('blastxml') and protein and nucleotide |
54 BLAST databases composite file formats ('blastdbp' and 'blastdbn'). | 61 BLAST databases composite file formats ('blastdbp' and 'blastdbn'). |
55 | 62 |
56 You must tell Galaxy about any system level BLAST databases using configuration | 63 As described above for an automated installation, you must also tell Galaxy |
57 files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein | 64 about any system level BLAST databases using the tool-data/blastdb*.loc files. |
58 databases like NR), located in the tool-data folder. Sample fils are included | |
59 which explain the tab based format to use. | |
60 | 65 |
61 You must install the NCBI BLAST+ standalone tools somewhere on the system | 66 You must install the NCBI BLAST+ standalone tools somewhere on the system |
62 path. Currently the unit tests are written using "BLAST 2.2.26+". | 67 path. Currently the unit tests are written using "BLAST 2.2.26+". |
63 | 68 |
64 Run the functional tests (adusting the section identifier to match your | 69 Run the functional tests (adjusting the section identifier to match your |
65 tool_conf.xml.sample file): | 70 tool_conf.xml.sample file): |
66 | 71 |
67 ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools | 72 ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools |
68 | 73 |
69 | 74 |
87 v0.0.16 - Added repository_dependencies.xml for automates installation of the | 92 v0.0.16 - Added repository_dependencies.xml for automates installation of the |
88 'blast_datatypes' repository from the Tool Shed. | 93 'blast_datatypes' repository from the Tool Shed. |
89 v0.0.17 - The BLAST+ search tools now default to extended tabular output | 94 v0.0.17 - The BLAST+ search tools now default to extended tabular output |
90 (all too often our users where having to re-run searches just to | 95 (all too often our users where having to re-run searches just to |
91 get one of the missing columns like query or subject length) | 96 get one of the missing columns like query or subject length) |
97 v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, | |
98 BLAST+ handling of some mult-file arguments is problematic). | |
99 v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc | |
100 for the domain databases they use (e.g. CDD, PFAM or SMART). | |
101 - Correct case of exception regular expression (for error handling | |
102 fall-back in case the return code is not set properly). | |
103 - Clearer naming of output files. | |
92 | 104 |
93 | 105 |
94 Developers | 106 Developers |
95 ========== | 107 ========== |
96 | 108 |
97 This script and related tools are being developed on the following hg branch: | 109 This script and related tools are being developed on the 'tools' branch of the |
98 http://bitbucket.org/peterjc/galaxy-central/src/tools | 110 following Mercurial repository: |
111 https://bitbucket.org/peterjc/galaxy-central/ | |
99 | 112 |
100 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use | 113 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use |
101 the following command from the Galaxy root folder: | 114 the following command from the Galaxy root folder: |
102 | 115 |
103 $ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh | 116 $ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh |
104 | 117 |
105 This similifies ensuring a consistent set of files is bundled each time, | 118 This simplifies ensuring a consistent set of files is bundled each time, |
106 including all the relevant test files. | 119 including all the relevant test files. |
107 | 120 |
108 | 121 |
109 Licence (MIT/BSD style) | 122 Licence (MIT/BSD style) |
110 ======================= | 123 ======================= |