| Previous changeset 6:e4c21444a3ba (2014-03-13) Next changeset 8:558a88cd49e4 (2014-03-13) |
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Commit message:
Bump SRA toolkit version |
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modified:
tool_dependencies.xml |
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| diff -r e4c21444a3ba -r e724bff23fb6 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 13 15:30:54 2014 -0400 +++ b/tool_dependencies.xml Thu Mar 13 16:08:12 2014 -0400 |
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| @@ -1,34 +1,34 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sra_toolkit" version="2.3.3-3"> + <package name="sra_toolkit" version="2.3.4-2"> <install version="1.0"> <actions> - <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action> + <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.4-2/sra_sdk-2.3.4-2.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">$INSTALL_DIR/ncbi/public</action> + <action type="make_directory">$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" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" 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. -This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. -When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a + <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. +This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. +When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a download of a large SRA data set. Build Requirements: - ar + ar bash make gcc, g++ libxml2 libcurl4 zlib - + On a debian based Linux OS use: apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev |