annotate tool_dependencies.xml @ 11:91558de676f4

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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
1 <?xml version="1.0"?>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
2 <tool_dependency>
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
3 <package name="sra_toolkit" version="2.4.5">
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
4 <install version="1.0">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
5 <actions>
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
6 <action type="set_environment">
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
7 <environment_variable name="NCBI" action="set_to">$PWD/ncbi</environment_variable>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
8 <environment_variable name="BUILD" action="set_to">$PWD/build</environment_variable>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
9 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib64</environment_variable>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
10 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib</environment_variable>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
11 </action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
12 <action type="make_directory">$BUILD</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
13 <action type="make_directory">$NCBI</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
14 <action type="change_directory">$NCBI</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
15 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
16 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
17 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
18 <action type="change_directory">$NCBI/ncbi-vdb</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
19 <action type="shell_command">git checkout bf5ffdd</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
20 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
21 <action type="change_directory">$NCBI/ngs</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
22 <action type="shell_command">git checkout 3a7a0ed</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
23 <action type="change_directory">$NCBI/ngs/ngs-sdk</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
24 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
25 <action type="change_directory">$NCBI/sra-tools</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
26 <action type="shell_command">git checkout 4ef7ea0</action>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
27 <action type="autoconf">--prefix=$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>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
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>
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
29 </actions>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
30 </install>
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
31 <readme>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
32 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
33 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
34 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
35 download of a large SRA data set.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
36
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
37 Build Requirements:
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
38 - make
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
39 - git
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
40 - gcc
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
41 - g++
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
42 - libxml2
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
43 - libcurl4
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
44 - zlib
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
45
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
46 On a debian based Linux OS use:
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
47
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
48 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
49
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
50 </readme>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
51 </package>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
52 </tool_dependency>