Mercurial > repos > rnateam > sortmerna

comparison tool_dependencies.xml @ 5:233da82dc31c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
author rnateam
date Wed, 09 Dec 2015 09:21:28 -0500
parents 42509ccf8f59
children 97f73e0566c9
comparison
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4:e6727cef3083 5:233da82dc31c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sortmerna" version="2.0"> 3 <package name="sortmerna" version="2.0">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions_group>
6 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> 6 <actions architecture="x86_64" os="linux">
7 <action type="autoconf"/> 7 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
8 <action type="set_environment"> 8 <action type="autoconf"/>
9 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable> 9 <action type="change_directory">../</action>
10 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 10 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
11 </action> 11 <action type="move_directory_files">
12 </actions> 12 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
13 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
14 </action>
15 <action type="set_environment">
16 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
18 </action>
19 </actions>
20 <actions architecture="x86_64" os="darwin">
21 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
22 <action type="shell_command"><![CDATA[
23 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install
24 ]]>
25 </action>
26 <action type="change_directory">../</action>
27 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
28 <action type="move_directory_files">
29 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
30 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
31 </action>
32 <action type="set_environment">
33 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
35 </action>
36 </actions>
37 </actions_group>
13 </install> 38 </install>
14 <readme> 39 <readme>
15 SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed. 40 SortMeRNA requires g++ 4.8 or later.
41
42 Note: the Clang compiler on Mac (distributed through Xcode) does not
43 support multithreading. The user is recommended to install the original
44 GCC compiler via MacPorts
16 </readme> 45 </readme>
17 </package> 46 </package>
18 </tool_dependency> 47 </tool_dependency>