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comparison tool_dependencies.xml @ 16:65412e4c5649 draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Sat, 15 Aug 2015 07:40:03 -0400
parents f382eaecfd34
children cf145d390fe3
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15:f382eaecfd34 16:65412e4c5649
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sra_toolkit" version="2.5.2"> 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="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz target_filename=ncbi-vdb-2.5.2.tar.gz</action> 6 <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz target_filename="ncbi-vdb-2.5.2.tar.gz"</action>
7 <action type="shell_command"> 7 <action type="shell_command">
8 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib 8 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
9 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 9 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
10 make 10 make
11 make install 11 make install
12 rm ../2.5.2.tar.gz 12 rm ../2.5.2.tar.gz
13 </action> 13 </action>
14 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz target_filename=ngs-1.1.3.tar.gz</action> 14 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz target_filename="ngs-1.1.3.tar.gz"</action>
15 <action type="shell_command"> 15 <action type="shell_command">
16 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib 16 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
17 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 17 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
18 make 18 make
19 make install 19 make install
20 </action> 20 </action>
21 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz target_filename=sra-tools-2.5.2.tar.gz</action> 21 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz target_filename="sra-tools-2.5.2.tar.gz"</action>
22 <action type="shell_command"> 22 <action type="shell_command">
23 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 23 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
24 sed -i -e "109s/-static//" tools/copycat/Makefile 24 sed -i -e "109s/-static//" tools/copycat/Makefile
25 make 25 make
26 make install 26 make install