Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison tool_dependencies.xml @ 21:847db227d9ce

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author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 21:11:03 -0400
parents 281f34ece271
children 4102c1600aa0
comparison
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20:281f34ece271 21:847db227d9ce
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 $INSTALL_DIR/ncbi-vdb
15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
16 make -j2
17 make install
18 cd $INSTALL_DIR/ngs/ngs-sdk
19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
20 make -j2
21 make install
22 cd $INSTALL_DIR/sra-tools
23 ./configure --prefix=$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
24 make -j2
25 make install
26 sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/lib64/ncbi/default.kfg
14 </action> 27 </action>
15 <action type="change_directory">./ncbi-vdb</action>
16 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
17 <action type="change_directory">../ngs/ngs-sdk</action>
18 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
19 <action type="change_directory">../../sra-tools</action>
20 <action type="shell_command">echo $PWD</action>
21 <action type="autoconf">--prefix=$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 --with-magic-prefix=/dev/null</action>
22 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
23 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> 28 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
24 </actions> 29 </actions>
25 </install> 30 </install>
26 <readme> 31 <readme>
27 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. 32 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.