Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 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 |
| files | tools/ncbi_blast_plus/blastxml_to_top_descr.txt tools/ncbi_blast_plus/datatypes_conf.xml |
| diffstat | 2 files changed, 32 insertions(+), 3 deletions(-) [+] |
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--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Thu Feb 07 14:56:18 2013 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Fri Feb 08 06:00:11 2013 -0500 @@ -1,7 +1,7 @@ Galaxy tool to extract top BLAST hit descriptions from BLAST XML ================================================================ -This tool is copyright 2012 by Peter Cock, The James Hutton Institute +This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -9,12 +9,23 @@ identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. -There are no additional dependancies. +This requires the 'blast_datatypes' repository from the Galaxy Tool Shed +to provide the 'blastxml' file format definition. + + +Automated Installation +====================== + +This should be straightforward, Galaxy should automatically install the +'blast_datatypes' dependency. + Manual Installation =================== +If you haven't done so before, first install the 'blast_datatypes' repository. + There are just two files to install (if doing this manually): * blastxml_to_top_descr.py (the Python script) @@ -37,6 +48,8 @@ ======= v0.0.1 - Initial version. +v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency + on the 'blast_datatypes' repository in the Tool Shed. Developers @@ -48,7 +61,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* +$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/datatypes_conf.xml Check this worked: @@ -56,6 +69,8 @@ tools/ncbi_blast_plus/blastxml_to_top_descr.py tools/ncbi_blast_plus/blastxml_to_top_descr.txt tools/ncbi_blast_plus/blastxml_to_top_descr.xml +tools/ncbi_blast_plus/datatypes_conf.xml + Licence (MIT/BSD style) =======================
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/datatypes_conf.xml Fri Feb 08 06:00:11 2013 -0500 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="blast.py"/> + </datatype_files> + <registration> + <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/> + <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/> + </registration> + <sniffers> + <sniffer type="galaxy.datatypes.blast:BlastXml"/> + </sniffers> +</datatypes>