Mercurial > repos > iuc > package_blast_plus_2_2_28
changeset 1:23b9ba41ad00 draft
Updated to use os/arch specific actions
| author | peterjc |
|---|---|
| date | Mon, 18 Nov 2013 05:42:38 -0500 |
| parents | ed85ca8e4295 |
| children | f5493f01911b |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 54 insertions(+), 19 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Oct 07 09:38:50 2013 -0400 +++ b/tool_dependencies.xml Mon Nov 18 05:42:38 2013 -0500 @@ -1,28 +1,63 @@ -<?xml version="1.0"?> +<?xml version='1.0' encoding='utf-8'?> <tool_dependency> <package name="blast+" version="2.2.28"> <install version="1.0"> - <actions> + <actions_group> + <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. --> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-universal-macosx.tar.gz</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. --> + <actions os="darwin" architecture="i386"> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-universal-macosx.tar.gz</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. --> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-x64-linux.tar.gz</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i386). --> + <actions os="linux" architecture="i386"> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-ia32-linux.tar.gz</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i686). --> + <actions os="linux" architecture="i686"> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-ia32-linux.tar.gz</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. --> + <actions> + <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action> + <action type="shell_command">echo Your machine details (the output from 'uname' and 'arch'):</action> + <action type="shell_command">uname</action> + <action type="shell_command">arch</action> + <action type="shell_command">echo Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!</action> + <action type="shell_command">false</action> + <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> + </actions> + <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> - <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default --> - <action type="shell_command"> - if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.28+-ia32-linux.tar.gz"; fi && - if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.28+-x64-linux.tar.gz"; fi && - if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.28+-universal-macosx.tar.gz"; fi && - echo Fetching $FILENAME && - if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/$FILENAME; fi && - if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/$FILENAME; fi && - tar -zxvf $FILENAME && - echo Downloaded and decompressed - </action> - <!-- move the binaries to the installation directory which is now on the $PATH --> - <action type="move_directory_files"> - <source_directory>ncbi-blast-2.2.28+/bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> + </actions_group> </install> <readme> Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+