Mercurial > repos > matt-shirley > sra_tools
view tool_dependencies.xml @ 40:f1b83804013f draft
add option to take plaintext file with accession on one line
author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 05 Aug 2013 09:40:26 -0400 |
parents | 7803126704c6 |
children | 88a13a2fd23f |
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<?xml version="1.0"?> <tool_dependency> <package name="sra_toolkit" version="2.3.2-4"> <install version="1.0"> <actions> <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action> <action type="shell_command">make release</action> <action type="shell_command">make static</action> <action type="shell_command">make</action> <action type="make_directory">$INSTALL_DIR/bin</action> <action type="make_directory">$INSTALL_DIR/ncbi</action> <action type="make_directory">$INSTALL_DIR/ncbi/public</action> <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" bin64/ncbi/default.kfg</action> <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> </actions> </install> <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. Various tools for working with SRA from NCBI. This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. Build Requirements: ar bash make gcc, g++ libxml2 libcurl4 zlib </readme> </package> </tool_dependency>