Mercurial > repos > peterjc > blastxml_to_top_descr
annotate tools/ncbi_blast_plus/blastxml_to_top_descr.txt @ 3:60c2d6ce926d draft
Uploaded v0.0.2b, with repository_dependencies.xml this time.
| author | peterjc |
|---|---|
| date | Fri, 08 Feb 2013 06:05:33 -0500 |
| parents | 44ecdccbe19d |
| children | 34a0adda2770 |
| rev | line source |
|---|---|
| 0 | 1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML |
| 2 ================================================================ | |
| 3 | |
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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 | |
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12 This requires the 'blast_datatypes' repository from the Galaxy Tool Shed |
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13 to provide the 'blastxml' file format definition. |
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14 |
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15 |
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16 Automated Installation |
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17 ====================== |
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18 |
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19 This should be straightforward, Galaxy should automatically install the |
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20 'blast_datatypes' dependency. |
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21 |
| 0 | 22 |
| 23 | |
| 24 Manual Installation | |
| 25 =================== | |
| 26 | |
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27 If you haven't done so before, first install the 'blast_datatypes' repository. |
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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. | |
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51 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency |
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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 | |
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Uploaded v0.0.2b, with repository_dependencies.xml this time.
peterjc
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64 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.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 | |
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peterjc
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72 tools/ncbi_blast_plus/repository_dependencies.xml |
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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. |