Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison tool_dependencies.xml @ 22:4102c1600aa0

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blargh
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 21:13:09 -0400
parents 847db227d9ce
children b94593ba997b
comparison
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21:847db227d9ce 22:4102c1600aa0
9 <action type="shell_command"> 9 <action type="shell_command">
10 git clone https://github.com/mdshw5/sra-tools.git 10 git clone https://github.com/mdshw5/sra-tools.git
11 git clone https://github.com/mdshw5/ncbi-vdb.git 11 git clone https://github.com/mdshw5/ncbi-vdb.git
12 git clone https://github.com/mdshw5/ngs.git 12 git clone https://github.com/mdshw5/ngs.git
13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib 13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
14 cd $INSTALL_DIR/ncbi-vdb 14 cd $INSTALL_DIR/src/ncbi-vdb
15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
16 make -j2 16 make -j2
17 make install 17 make install
18 cd $INSTALL_DIR/ngs/ngs-sdk 18 cd $INSTALL_DIR/ngs/ngs-sdk
19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build 19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
20 make -j2 20 make -j2
21 make install 21 make install
22 cd $INSTALL_DIR/sra-tools 22 cd $INSTALL_DIR/src/sra-tools
23 ./configure --prefix=$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 23 ./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=$INSTALL_DIR
24 make -j2 24 make -j2
25 make install 25 make install
26 sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/lib64/ncbi/default.kfg 26 sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/lib64/ncbi/default.kfg
27 </action> 27 </action>