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comparison tool_dependencies.xml @ 11:91558de676f4

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Update to latest toolkit version - fix installation issues.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 14:06:16 -0400
parents 16f96ab0196b
children d45b5bdcff3f
comparison
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10:16f96ab0196b 11:91558de676f4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sra_toolkit" version="2.4.3"> 3 <package name="sra_toolkit" version="2.4.5">
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/current/sratoolkit.current.version</action> 6 <action type="set_environment">
7 <action type="shell_command">make release</action> 7 <environment_variable name="NCBI" action="set_to">$PWD/ncbi</environment_variable>
8 <action type="shell_command">make static</action> 8 <environment_variable name="BUILD" action="set_to">$PWD/build</environment_variable>
9 <action type="shell_command">make</action> 9 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib64</environment_variable>
10 <action type="make_directory">$INSTALL_DIR/bin</action> 10 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib</environment_variable>
11 <action type="make_directory">$INSTALL_DIR/ncbi</action> 11 </action>
12 <action type="make_directory">$INSTALL_DIR/ncbi/public</action> 12 <action type="make_directory">$BUILD</action>
13 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> 13 <action type="make_directory">$NCBI</action>
14 <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> 14 <action type="change_directory">$NCBI</action>
15 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> 15 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
16 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
17 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
18 <action type="change_directory">$NCBI/ncbi-vdb</action>
19 <action type="shell_command">git checkout bf5ffdd</action>
20 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
21 <action type="change_directory">$NCBI/ngs</action>
22 <action type="shell_command">git checkout 3a7a0ed</action>
23 <action type="change_directory">$NCBI/ngs/ngs-sdk</action>
24 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
25 <action type="change_directory">$NCBI/sra-tools</action>
26 <action type="shell_command">git checkout 4ef7ea0</action>
27 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD --with-ncbi-vdb-build=$BUILD --with-ncbi-vdb-sources=$NCBI/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
28 <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>
16 </actions> 29 </actions>
17 </install> 30 </install>
18 <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. 31 <readme>
32 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. 33 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 34 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. 35 download of a large SRA data set.
22 36
23 Build Requirements: 37 Build Requirements:
24 ar 38 - make
25 bash 39 - git
26 make 40 - gcc
27 gcc, g++ 41 - g++
28 libxml2 42 - libxml2
29 libcurl4 43 - libcurl4
30 zlib 44 - zlib
31 45
32 On a debian based Linux OS use: 46 On a debian based Linux OS use:
33 47
34 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev 48 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
49
35 </readme> 50 </readme>
36 </package> 51 </package>
37 </tool_dependency> 52 </tool_dependency>