| Previous changeset 23:2c70fed75e57 (2013-08-05) Next changeset 25:949fa0294c0d (2013-08-07) |
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Commit message:
Uploaded v0.0.20pre15, try platform selection installation via shell commands. |
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modified:
ncbi_blast_plus/README.rst ncbi_blast_plus/tool_dependencies.xml |
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| diff -r 2c70fed75e57 -r 5693417851ec ncbi_blast_plus/README.rst --- a/ncbi_blast_plus/README.rst Mon Aug 05 16:03:58 2013 -0400 +++ b/ncbi_blast_plus/README.rst Tue Aug 06 12:04:54 2013 -0400 |
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| @@ -115,8 +115,7 @@ - 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). + - Auto-installation uses the NCBI supplied pre-compiled binaries. ======= ====================================================================== |
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| diff -r 2c70fed75e57 -r 5693417851ec ncbi_blast_plus/tool_dependencies.xml --- a/ncbi_blast_plus/tool_dependencies.xml Mon Aug 05 16:03:58 2013 -0400 +++ b/ncbi_blast_plus/tool_dependencies.xml Tue Aug 06 12:04:54 2013 -0400 |
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| @@ -3,23 +3,30 @@ <package name="blast+" version="2.2.26+"> <install version="1.0"> <actions> - <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="i686">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> - <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR/ncbi-blast-2.2.26+ && make && make install</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default --> + <action type="shell_command">if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi</action> + <action type="shell_command">if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi</action> + <action type="shell_command">if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi</action> + <!-- now download and unzip it, assuming can't use $FILENAME in the Tool Shed action? --> + <action type="shell_command">wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME</action> + <action type="shell_command">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> -These links provide information for building the NCBI Blast+ package in most environments. +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. -System requirements +For more details, see: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download </readme> </package> |