Mercurial > repos > iuc > package_blast_plus_2_2_26
diff tool_dependencies.xml @ 2:0e536576294c draft
Experimental shell script solution to downloading appropriate binaries.
| author | peterjc |
|---|---|
| date | Wed, 14 Aug 2013 09:07:45 -0400 |
| parents | 9ff9bfdcd04f |
| children | c85236cd100d |
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--- a/tool_dependencies.xml Mon Aug 12 06:02:46 2013 -0400 +++ b/tool_dependencies.xml Wed Aug 14 09:07:45 2013 -0400 @@ -1,27 +1,35 @@ <?xml version="1.0"?> <tool_dependency> - <package name="boost" version="1.53.0"> - <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> <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> - <!-- populate the environment variables from the dependent repos --> - <action type="set_environment_for_install"> - <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="boost" version="1.53.0" /> - </repository> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> - <action type="shell_command">cd c++ && ./configure --with-boost=$BOOST_ROOT_DIR --prefix=$INSTALL_DIR && make && make install</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default --> + <action type="shell_command"> + if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi && + if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi && + if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi && + echo Fetching $FILENAME && + if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi && + if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi && + tar -zxvf $FILENAME && + </action> + <!-- move the binaries to the installation directory which is now on the $PATH --> + <action type="move_directory_files"> + <source_directory>ncbi-blast-2.2.26+/bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> </action> </actions> </install> <readme> -Downloads and compiles BLAST+ from the NCBI, which assumes you have -all the required build dependencies installed. See: +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. + +For more details, see: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download </readme> </package>
