Mercurial > repos > bebatut > sortmerna

comparison tool_dependencies.xml @ 15:baab049d3aff draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
author bebatut
date Wed, 10 Feb 2016 04:02:18 -0500
parents 011ec5258e71
children
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14:011ec5258e71 15:baab049d3aff
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_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-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
8 <action type="autoconf"/> 8 <action type="shell_command"><![CDATA[
9 ./build.sh --prefix=$INSTALL_DIR
10 ]]>
11 </action>
9 <action type="change_directory">../</action> 12 <action type="change_directory">../</action>
10 <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action> 13 <action type="make_directory">$INSTALL_DIR/bin/</action>
14 <action type="move_file">
15 <source>sortmerna-2.0/sortmerna</source>
16 <destination>$INSTALL_DIR/bin</destination>
17 </action>
18 <action type="move_file">
19 <source>sortmerna-2.0/indexdb_rna</source>
20 <destination>$INSTALL_DIR/bin</destination>
21 </action>
22 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
11 <action type="move_directory_files"> 23 <action type="move_directory_files">
12 <source_directory>sortmerna-2.0/</source_directory> 24 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
13 <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory> 25 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
14 </action> 26 </action>
15 <action type="set_environment"> 27 <action type="set_environment">
16 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable> 28 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
18 </action> 30 </action>
19 </actions> 31 </actions>
20 <actions architecture="x86_64" os="darwin"> 32 <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> 33 <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[ 34 <action type="shell_command"><![CDATA[
23 export CC=clang && export CXX=clang++ && ./configure && make && make install 35 export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install
24 ]]> 36 ]]>
25 </action> 37 </action>
26 <action type="change_directory">../</action> 38 <action type="change_directory">../</action>
27 <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action> 39 <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
28 <action type="move_directory_files"> 40 <action type="move_directory_files">
29 <source_directory>sortmerna-2.0/</source_directory> 41 <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
30 <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory> 42 <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
31 </action> 43 </action>
32 <action type="set_environment"> 44 <action type="set_environment">
33 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable> 45 <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
35 </action> 47 </action>
36 </actions> 48 </actions>
37 </actions_group> 49 </actions_group>
38 </install> 50 </install>
39 <readme> 51 <readme>
40 SortMeRNA requires g++ 4.3 or later. 52 SortMeRNA requires g++ 4.8 or later.
41 53
42 Note: the Clang compiler on Mac (distributed through Xcode) does not 54 Note: the Clang compiler on Mac (distributed through Xcode) does not
43 support multithreading. The user is recommended to install the original 55 support multithreading. The user is recommended to install the original
44 GCC compiler via MacPorts 56 GCC compiler via MacPorts
45 </readme> 57 </readme>