Mercurial > repos > rnateam > sortmerna

comparison tool_dependencies.xml @ 6:97f73e0566c9 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 06:53:28 -0400
parents 233da82dc31c
children
comparison
equal deleted inserted replaced
5:233da82dc31c 6:97f73e0566c9
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_group> 5 <actions_group>
6 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> 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="autoconf"/> 8 <action type="shell_command"><![CDATA[
9 <action type="change_directory">../</action> 9 ./build.sh --prefix=$INSTALL_DIR
10 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action> 10 ]]>
11 <action type="move_directory_files"> 11 </action>
12 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory> 12 <action type="shell_command">make install</action>
13 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory> 13 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
14 </action> 14 <action type="move_directory_files">
15 <action type="set_environment"> 15 <source_directory>rRNA_databases/</source_directory>
16 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable> 16 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 17 </action>
18 </action> 18 <action type="set_environment">
19 </actions> 19 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
21 </action>
22 </actions>
20 <actions architecture="x86_64" os="darwin"> 23 <actions architecture="x86_64" os="darwin">
21 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> 24 <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
22 <action type="shell_command"><![CDATA[ 25 <action type="shell_command"><![CDATA[
23 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install 26 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install
24 ]]> 27 ]]>
25 </action> 28 </action>
26 <action type="change_directory">../</action> 29 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
27 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action> 30 <action type="move_directory_files">
28 <action type="move_directory_files"> 31 <source_directory>rRNA_databases/</source_directory>
29 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory> 32 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
30 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory> 33 </action>
31 </action> 34 <action type="set_environment">
32 <action type="set_environment"> 35 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
33 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable> 36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 37 </action>
35 </action> 38 </actions>
36 </actions> 39 </actions_group>
37 </actions_group>
38 </install> 40 </install>
39 <readme> 41 <readme>
40 SortMeRNA requires g++ 4.8 or later. 42 SortMeRNA requires g++ 4.8 or later.
41 43
42 Note: the Clang compiler on Mac (distributed through Xcode) does not 44 Note: the Clang compiler on Mac (distributed through Xcode) does not
43 support multithreading. The user is recommended to install the original 45 support multithreading. The user is recommended to install the original
44 GCC compiler via MacPorts 46 GCC compiler via MacPorts
45 </readme> 47 </readme>
46 </package> 48 </package>
47 </tool_dependency> 49 </tool_dependency>