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comparison tool_dependencies.xml @ 2:2c5483e80fb7 draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 12:48:14 -0400
parents 29892b1d24b9
children fb21b2e48a1e
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1:29892b1d24b9 2:2c5483e80fb7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sra_toolkit" version="2.4.5"> 3 <package name="sra_toolkit" version="2.5.2">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="make_directory">src</action> 6 <action type="make_directory">src</action>
7 <action type="make_directory">build</action> 7 <action type="make_directory">build</action>
8 <action type="change_directory">src</action> 8 <action type="change_directory">src</action>
9 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
9 <action type="shell_command"> 10 <action type="shell_command">
10 git clone https://github.com/mdshw5/sra-tools.git 11 tar -xf 2.5.2.tar.gz
11 git clone https://github.com/mdshw5/ncbi-vdb.git 12 rm 2.5.2.tar.gz
12 git clone https://github.com/mdshw5/ngs.git 13 mv sra-tools-2.5.2 sra-tools
14 </action>
15 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
16 <action type="shell_command">
17 tar -xf 1.1.3.tar.gz
18 rm 1.1.3.tar.gz
19 mv ngs-1.1.3 ngs
20 </action>
21 <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
22 <action type="shell_command">
23 tar -xf 2.5.2.tar.gz
24 rm 2.5.2.tar.gz
25 mv ncbi-vdb-2.5.2 ncbi-vdb
26 </action>
27 <action type="shell_command">
13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib 28 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
14 cd $INSTALL_DIR/src/ncbi-vdb 29 cd $INSTALL_DIR/src/ncbi-vdb
15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 30 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
16 make 31 make
17 make install 32 make install