Mercurial > repos > peterjc > blastxml_to_top_descr
comparison tools/ncbi_blast_plus/blastxml_to_top_descr.txt @ 1:dff89c7e4308 draft
Uploaded v0.0.2, declared dependency on blast_datatypes
author | peterjc |
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date | Fri, 08 Feb 2013 06:00:11 -0500 |
parents | 075fe5424c32 |
children | 44ecdccbe19d |
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0:075fe5424c32 | 1:dff89c7e4308 |
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1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML | 1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML |
2 ================================================================ | 2 ================================================================ |
3 | 3 |
4 This tool is copyright 2012 by Peter Cock, The James Hutton Institute | 4 This tool is copyright 2012-2013 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 This tool is a short Python script to parse a BLAST XML file, and extract the | 8 This tool is a short Python script to parse a BLAST XML file, and extract the |
9 identifiers with description for the top matches (by default the top 3), and | 9 identifiers with description for the top matches (by default the top 3), and |
10 output these as a simple tabular file along with the query identifiers. | 10 output these as a simple tabular file along with the query identifiers. |
11 | 11 |
12 There are no additional dependancies. | 12 This requires the 'blast_datatypes' repository from the Galaxy Tool Shed |
13 to provide the 'blastxml' file format definition. | |
14 | |
15 | |
16 Automated Installation | |
17 ====================== | |
18 | |
19 This should be straightforward, Galaxy should automatically install the | |
20 'blast_datatypes' dependency. | |
21 | |
13 | 22 |
14 | 23 |
15 Manual Installation | 24 Manual Installation |
16 =================== | 25 =================== |
26 | |
27 If you haven't done so before, first install the 'blast_datatypes' repository. | |
17 | 28 |
18 There are just two files to install (if doing this manually): | 29 There are just two files to install (if doing this manually): |
19 | 30 |
20 * blastxml_to_top_descr.py (the Python script) | 31 * blastxml_to_top_descr.py (the Python script) |
21 * blastxml_to_top_descr.xml (the Galaxy tool definition) | 32 * blastxml_to_top_descr.xml (the Galaxy tool definition) |
35 | 46 |
36 History | 47 History |
37 ======= | 48 ======= |
38 | 49 |
39 v0.0.1 - Initial version. | 50 v0.0.1 - Initial version. |
51 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency | |
52 on the 'blast_datatypes' repository in the Tool Shed. | |
40 | 53 |
41 | 54 |
42 Developers | 55 Developers |
43 ========== | 56 ========== |
44 | 57 |
46 http://bitbucket.org/peterjc/galaxy-central/src/tools | 59 http://bitbucket.org/peterjc/galaxy-central/src/tools |
47 | 60 |
48 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | 61 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
49 the following command from the Galaxy root folder: | 62 the following command from the Galaxy root folder: |
50 | 63 |
51 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* | 64 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/datatypes_conf.xml |
52 | 65 |
53 Check this worked: | 66 Check this worked: |
54 | 67 |
55 $ tar -tzf blastxml_to_top_descr.tar.gz | 68 $ tar -tzf blastxml_to_top_descr.tar.gz |
56 tools/ncbi_blast_plus/blastxml_to_top_descr.py | 69 tools/ncbi_blast_plus/blastxml_to_top_descr.py |
57 tools/ncbi_blast_plus/blastxml_to_top_descr.txt | 70 tools/ncbi_blast_plus/blastxml_to_top_descr.txt |
58 tools/ncbi_blast_plus/blastxml_to_top_descr.xml | 71 tools/ncbi_blast_plus/blastxml_to_top_descr.xml |
72 tools/ncbi_blast_plus/datatypes_conf.xml | |
73 | |
59 | 74 |
60 Licence (MIT/BSD style) | 75 Licence (MIT/BSD style) |
61 ======================= | 76 ======================= |
62 | 77 |
63 Permission to use, copy, modify, and distribute this software and its | 78 Permission to use, copy, modify, and distribute this software and its |