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comparison tool_dependencies.xml @ 10:472f8a7e13b3 draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 13:30:47 -0400
parents 9c04607bbb08
children 833f4feaee33
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9:9c04607bbb08 10:472f8a7e13b3
11 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib 11 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
12 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 12 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
13 make 13 make
14 make install 14 make install
15 </action> 15 </action>
16 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
17 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action> 16 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
18 <action type="change_directory">../src</action>
19 <action type="shell_command"> 17 <action type="shell_command">
20 ls
21 mv sra-tools-2.5.2 sra-tools
22 mv ngs-1.1.3 ngs
23 mv ncbi-vdb-2.5.2 ncbi-vdb
24 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib 18 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
25 cd $INSTALL_DIR/src/ncbi-vdb
26 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
27 make 20 make
28 make install 21 make install
29 cd $INSTALL_DIR/src/ngs/ngs-sdk 22 </action>
30 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 23 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
31 make 24 <action type="shell_command">
32 make install 25 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build
33 cd $INSTALL_DIR/src/sra-tools
34 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR
35 sed -i -e "109s/-static//" tools/copycat/Makefile 26 sed -i -e "109s/-static//" tools/copycat/Makefile
36 make 27 make
37 make install 28 make install
38 cd $INSTALL_DIR/bin 29 cd $INSTALL_DIR/bin
39 ./vdb-config -s "/repository/user/main/public/cache-enabled=false" 30 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
40 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR" 31 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
41 </action> 32 </action>
33 <!-- <action type="change_directory">../src</action> -->
42 <action type="set_environment"> 34 <action type="set_environment">
43 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 35 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
44 </action> 36 </action>
45 </actions> 37 </actions>
46 </install> 38 </install>