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comparison tools/ncbi_blast_plus/blastxml_to_top_descr.txt @ 1:dff89c7e4308 draft

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Uploaded v0.0.2, declared dependency on blast_datatypes
author peterjc
date Fri, 08 Feb 2013 06:00:11 -0500
parents 075fe5424c32
children 44ecdccbe19d
comparison
equal deleted inserted replaced
0:075fe5424c32 1:dff89c7e4308
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