Mercurial > repos > rnateam > sortmerna

comparison tool_dependencies.xml @ 2:3699b6b771e0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
author rnateam
date Tue, 29 Mar 2016 07:01:13 -0400
parents b482293b2987
children
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1:b482293b2987 2:3699b6b771e0
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="2.1b">
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-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
8 <action type="set_environment"> 8 <action type="shell_command"><![CDATA[
9 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable> 9 ./build.sh --prefix=$INSTALL_DIR
10 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 10 ]]>
11 </action> 11 </action>
12 </actions> 12 <action type="shell_command">make install</action>
13 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
14 <action type="move_directory_files">
15 <source_directory>rRNA_databases/</source_directory>
16 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
17 </action>
18 <action type="set_environment">
19 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
21 </action>
22 </actions>
23 <actions architecture="x86_64" os="darwin">
24 <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
25 <action type="shell_command"><![CDATA[
26 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install
27 ]]>
28 </action>
29 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
30 <action type="move_directory_files">
31 <source_directory>rRNA_databases/</source_directory>
32 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
33 </action>
34 <action type="set_environment">
35 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
37 </action>
38 </actions>
39 </actions_group>
13 </install> 40 </install>
14 <readme> 41 <readme>
15 SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed. 42 SortMeRNA requires g++ 4.8 or later.
43
44 Note: the Clang compiler on Mac (distributed through Xcode) does not
45 support multithreading. The user is recommended to install the original
46 GCC compiler via MacPorts
16 </readme> 47 </readme>
17 </package> 48 </package>
18 </tool_dependency> 49 </tool_dependency>