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update to SRA toolkit 2.3.3-3
author Matt Shirley <mdshw5@gmail.com>
date Mon, 16 Sep 2013 20:27:28 -0400
parents 88a13a2fd23f
children
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46:88a13a2fd23f 47:04cc8176e86f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sra_toolkit" version="2.3.2-4"> 3 <package name="sra_toolkit" version="2.3.3-3">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <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> 6 <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>
7 <action type="shell_command">make release</action> 7 <action type="shell_command">make release</action>
8 <action type="shell_command">make static</action> 8 <action type="shell_command">make static</action>
9 <action type="shell_command">make</action> 9 <action type="shell_command">make</action>
10 <action type="make_directory">$INSTALL_DIR/bin</action> 10 <action type="make_directory">$INSTALL_DIR/bin</action>
11 <action type="make_directory">$INSTALL_DIR/ncbi</action> 11 <action type="make_directory">$INSTALL_DIR/ncbi</action>
12 <action type="make_directory">$INSTALL_DIR/ncbi/public</action> 12 <action type="make_directory">$INSTALL_DIR/ncbi/public</action>
13 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> 13 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action>
14 <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> 14 <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
15 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> 15 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
16 </actions> 16 </actions>
17 </install> 17 </install>
18 <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. 18 <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
19 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. 19 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
20 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a 20 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a