Mercurial > repos > qfab > package_mothur
comparison tool_dependencies.xml @ 0:150982d8fd53 draft default tip
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| author | qfab |
|---|---|
| date | Fri, 30 May 2014 02:15:54 -0400 |
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| -1:000000000000 | 0:150982d8fd53 |
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| 1 <?xml version='1.0' encoding='utf-8'?> | |
| 2 <tool_dependency> | |
| 3 <package name="mothur" version="1.30.2-1.33.3"> | |
| 4 <install version="1.0"> | |
| 5 <actions_group> | |
| 6 <!-- Download the binaries for mothur compatible with 64-bit OSX. --> | |
| 7 <actions os="darwin" architecture="x86_64"> | |
| 8 <action type="download_by_url">http://www.mothur.org/w/images/f/fb/Mothur.mac_64.OSX-10.6.zip</action> | |
| 9 <action type="move_directory_files"> | |
| 10 <source_directory>mothur</source_directory> | |
| 11 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 12 </action> | |
| 13 </actions> | |
| 14 <!-- Download the binaries for mothur compatible with 64-bit Linux. --> | |
| 15 <actions os="linux" architecture="x86_64"> | |
| 16 <!-- use version 1.30.2 due to problems with OSX releases before 6 --> | |
| 17 <!-- <action type="download_by_url">http://www.mothur.org/w/images/4/46/Mothur.cen_64.zip</action> --> | |
| 18 <action type="download_by_url">https://bitbucket.org/qfab/metagenomics/downloads/Mothur.cen_64.zip</action> | |
| 19 <action type="move_directory_files"> | |
| 20 <source_directory>mothur</source_directory> | |
| 21 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 22 </action> | |
| 23 </actions> | |
| 24 <!-- Download the binaries for mothur compatible with 32-bit Linux. --> | |
| 25 <actions os="linux" architecture="i386"> | |
| 26 <action type="download_by_url">www.mothur.org/w/images/1/13/Mothur.cen.zip</action> | |
| 27 <action type="move_directory_files"> | |
| 28 <source_directory>mothur</source_directory> | |
| 29 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 30 </action> | |
| 31 </actions> | |
| 32 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. --> | |
| 33 <actions> | |
| 34 <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action> | |
| 35 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action> | |
| 36 <action type="shell_command">uname</action> | |
| 37 <action type="shell_command">arch</action> | |
| 38 <action type="shell_command">echo Please report this via support@qfab.org - thank you!</action> | |
| 39 <action type="shell_command">false</action> | |
| 40 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> | |
| 41 </actions> | |
| 42 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> | |
| 43 <action type="shell_command">chmod ugo+x $INSTALL_DIR/mothur</action> | |
| 44 <action type="set_environment"> | |
| 45 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> | |
| 46 </action> | |
| 47 </actions_group> | |
| 48 </install> | |
| 49 <readme> | |
| 50 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. | |
| 51 </readme> | |
| 52 </package> | |
| 53 </tool_dependency> |