Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 2:44ecdccbe19d draft
Uploaded v0.0.2a, fixed dependency declaration
| author | peterjc |
|---|---|
| date | Fri, 08 Feb 2013 06:02:35 -0500 |
| parents | dff89c7e4308 |
| children | 60c2d6ce926d |
| files | tools/ncbi_blast_plus/blastxml_to_top_descr.txt tools/ncbi_blast_plus/datatypes_conf.xml tools/ncbi_blast_plus/tool_dependencies.xml |
| diffstat | 3 files changed, 23 insertions(+), 16 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Fri Feb 08 06:00:11 2013 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Fri Feb 08 06:02:35 2013 -0500 @@ -61,7 +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.* tools/ncbi_blast_plus/datatypes_conf.xml +$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/tool_dependencies.xml Check this worked: @@ -69,7 +69,7 @@ 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 +tools/ncbi_blast_plus/tool_dependencies.xml Licence (MIT/BSD style)
--- a/tools/ncbi_blast_plus/datatypes_conf.xml Fri Feb 08 06:00:11 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Fri Feb 08 06:02:35 2013 -0500 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="blast+" version="2.2.26+"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> + <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the NCBI Blast+ package in most environments. + +System requirements +http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download + </readme> + </package> +</tool_dependency> +