Mercurial > repos > peterjc > blastxml_to_top_descr
annotate tools/ncbi_blast_plus/blastxml_to_top_descr.txt @ 1:dff89c7e4308 draft
Uploaded v0.0.2, declared dependency on blast_datatypes
author | peterjc |
---|---|
date | Fri, 08 Feb 2013 06:00:11 -0500 |
parents | 075fe5424c32 |
children | 44ecdccbe19d |
rev | line source |
---|---|
0 | 1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML |
2 ================================================================ | |
3 | |
1
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
4 This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute |
0 | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
6 See the licence text below. | |
7 | |
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 | |
10 output these as a simple tabular file along with the query identifiers. | |
11 | |
1
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
12 This requires the 'blast_datatypes' repository from the Galaxy Tool Shed |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
13 to provide the 'blastxml' file format definition. |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
14 |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
15 |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
16 Automated Installation |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
17 ====================== |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
18 |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
19 This should be straightforward, Galaxy should automatically install the |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
20 'blast_datatypes' dependency. |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
21 |
0 | 22 |
23 | |
24 Manual Installation | |
25 =================== | |
26 | |
1
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
27 If you haven't done so before, first install the 'blast_datatypes' repository. |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
28 |
0 | 29 There are just two files to install (if doing this manually): |
30 | |
31 * blastxml_to_top_descr.py (the Python script) | |
32 * blastxml_to_top_descr.xml (the Galaxy tool definition) | |
33 | |
34 The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to | |
35 the NCBI BLAST+ tool wrappers. | |
36 | |
37 You will also need to modify the tools_conf.xml file to tell Galaxy to offer | |
38 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line: | |
39 | |
40 <tool file="filters/seq_select_by_id.xml" /> | |
41 | |
42 To run the tool's tests, also add this line to tools_conf.xml.sample then: | |
43 | |
44 $ sh run_functional_tests.sh -id blastxml_to_top_descr | |
45 | |
46 | |
47 History | |
48 ======= | |
49 | |
50 v0.0.1 - Initial version. | |
1
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
51 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
52 on the 'blast_datatypes' repository in the Tool Shed. |
0 | 53 |
54 | |
55 Developers | |
56 ========== | |
57 | |
58 This script and related tools are being developed on the following hg branch: | |
59 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
60 | |
61 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
62 the following command from the Galaxy root folder: | |
63 | |
1
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
64 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/datatypes_conf.xml |
0 | 65 |
66 Check this worked: | |
67 | |
68 $ tar -tzf blastxml_to_top_descr.tar.gz | |
69 tools/ncbi_blast_plus/blastxml_to_top_descr.py | |
70 tools/ncbi_blast_plus/blastxml_to_top_descr.txt | |
71 tools/ncbi_blast_plus/blastxml_to_top_descr.xml | |
1
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
72 tools/ncbi_blast_plus/datatypes_conf.xml |
dff89c7e4308
Uploaded v0.0.2, declared dependency on blast_datatypes
peterjc
parents:
0
diff
changeset
|
73 |
0 | 74 |
75 Licence (MIT/BSD style) | |
76 ======================= | |
77 | |
78 Permission to use, copy, modify, and distribute this software and its | |
79 documentation with or without modifications and for any purpose and | |
80 without fee is hereby granted, provided that any copyright notices | |
81 appear in all copies and that both those copyright notices and this | |
82 permission notice appear in supporting documentation, and that the | |
83 names of the contributors or copyright holders not be used in | |
84 advertising or publicity pertaining to distribution of the software | |
85 without specific prior permission. | |
86 | |
87 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
88 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
89 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
90 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
91 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
92 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
93 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
94 OR PERFORMANCE OF THIS SOFTWARE. |