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Commit message:
Uploaded |
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added:
tool_dependencies.xml |
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| diff -r 000000000000 -r 150982d8fd53 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri May 30 02:15:54 2014 -0400 |
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| @@ -0,0 +1,53 @@ +<?xml version='1.0' encoding='utf-8'?> + <tool_dependency> + <package name="mothur" version="1.30.2-1.33.3"> + <install version="1.0"> + <actions_group> + <!-- Download the binaries for mothur compatible with 64-bit OSX. --> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url">http://www.mothur.org/w/images/f/fb/Mothur.mac_64.OSX-10.6.zip</action> + <action type="move_directory_files"> + <source_directory>mothur</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- Download the binaries for mothur compatible with 64-bit Linux. --> + <actions os="linux" architecture="x86_64"> + <!-- use version 1.30.2 due to problems with OSX releases before 6 --> + <!-- <action type="download_by_url">http://www.mothur.org/w/images/4/46/Mothur.cen_64.zip</action> --> + <action type="download_by_url">https://bitbucket.org/qfab/metagenomics/downloads/Mothur.cen_64.zip</action> + <action type="move_directory_files"> + <source_directory>mothur</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <!-- Download the binaries for mothur compatible with 32-bit Linux. --> + <actions os="linux" architecture="i386"> + <action type="download_by_url">www.mothur.org/w/images/1/13/Mothur.cen.zip</action> + <action type="move_directory_files"> + <source_directory>mothur</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 support@qfab.org - 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="shell_command">chmod ugo+x $INSTALL_DIR/mothur</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> + Downloads the precompiled 32bit Linux, 64bit Linux, or Mac 64-bit OS X mothur binaries, 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. + </readme> + </package> + </tool_dependency> |