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comparison tool_dependencies.xml @ 7:e724bff23fb6

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Bump SRA toolkit version
author Matt Shirley <mdshw5@gmail.com>
date Thu, 13 Mar 2014 16:08:12 -0400
parents 293927a46697
children 16f96ab0196b
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6:e4c21444a3ba 7:e724bff23fb6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sra_toolkit" version="2.3.3-3"> 3 <package name="sra_toolkit" version="2.3.4-2">
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/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action> 6 <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>
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
21 download of a large SRA data set. 21 download of a large SRA data set.
22 22
23 Build Requirements: 23 Build Requirements:
24 ar 24 ar
25 bash 25 bash
26 make 26 make
27 gcc, g++ 27 gcc, g++
28 libxml2 28 libxml2
29 libcurl4 29 libcurl4
30 zlib 30 zlib
31 31
32 On a debian based Linux OS use: 32 On a debian based Linux OS use:
33 33
34 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev 34 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
35 </readme> 35 </readme>
36 </package> 36 </package>