Mercurial > repos > peterjc > ncbi_blast_plus
changeset 22:9b8b2817f411 draft
Uploaded v0.0.20pre13, auto-installation script from Dave Bouvier
| author | peterjc |
|---|---|
| date | Mon, 05 Aug 2013 14:29:58 -0400 |
| parents | 6902315b7730 |
| children | 2c70fed75e57 |
| files | ncbi_blast_plus/README.rst ncbi_blast_plus/tool_dependencies.xml |
| diffstat | 2 files changed, 10 insertions(+), 15 deletions(-) [+] |
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--- a/ncbi_blast_plus/README.rst Mon Aug 05 12:39:59 2013 -0400 +++ b/ncbi_blast_plus/README.rst Mon Aug 05 14:29:58 2013 -0400 @@ -115,6 +115,8 @@ - Tweak dependency on blast_datatypes to also work on Test Tool Shed - Adopted standard MIT License. - Development moved to GitHub, https://github.com/peterjc/galaxy_blast + - Auto-installation tries to use the NCBI supplied binaries, falling + back on local compilation from source if required (Dave Bouvier). ======= ======================================================================
--- a/ncbi_blast_plus/tool_dependencies.xml Mon Aug 05 12:39:59 2013 -0400 +++ b/ncbi_blast_plus/tool_dependencies.xml Mon Aug 05 14:29:58 2013 -0400 @@ -3,31 +3,24 @@ <package name="blast+" version="2.2.26+"> <install version="1.0"> <actions> - <action type="download_by_url"> + <action type="download_binary"> + <url_template os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template> <url_template os="linux" architecture="x86_64">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</url_template> - <url_template os="linux" architecture="i386">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template> + <url_template os="linux" architecture="ia32">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template> <url_template os="linux" architecture="i686">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template> - <url_template os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template> </action> - <action type="move_directory_files"> - <!-- Galaxy will have changed directory into ncbi-blast-2.2.26+/ --> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> + <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR/ncbi-blast-2.2.26+ && make && make install</action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> -Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+ -binaries from the NCBI, which is faster than performing a local compliation, -avoids any issues with build dependencies, and is more reproducible between -installations as there is no variability from the compiler or library versions. +These links provide information for building the NCBI Blast+ package in most environments. -For more details, see: +System requirements http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download </readme> </package> </tool_dependency> -