Mercurial > repos > matt-shirley > ncbi_sra_toolkit

annotate tool_dependencies.xml @ 18:3da3d1a4deae

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Back to shell commands. Maybe change_directory directive does not support reading env variables?
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 20:31:50 -0400
parents a8261e9cbe13
children 6d25dfb4dbb4
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">
14
ef71f5982df5 Should have linked the damn thing.
Matt Shirley <mdshw5@gmail.com>
parents: 13
diff changeset
5 <actions>
15
c71031b17e08 Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents: 14
diff changeset
6 <action type="make_directory">src</action>
c71031b17e08 Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents: 14
diff changeset
7 <action type="make_directory">build</action>
c71031b17e08 Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents: 14
diff changeset
8 <action type="change_directory">src</action>
16
dd337a830b5c Use patched versions of tools.
Matt Shirley <mdshw5@gmail.com>
parents: 15
diff changeset
9 <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action>
dd337a830b5c Use patched versions of tools.
Matt Shirley <mdshw5@gmail.com>
parents: 15
diff changeset
10 <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action>
dd337a830b5c Use patched versions of tools.
Matt Shirley <mdshw5@gmail.com>
parents: 15
diff changeset
11 <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action>
13
3369a52a5934 Set environment variables using shell.
Matt Shirley <mdshw5@gmail.com>
parents: 12
diff changeset
12 <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action>
18
3da3d1a4deae Back to shell commands. Maybe change_directory directive does not support reading env variables?
Matt Shirley <mdshw5@gmail.com>
parents: 17
diff changeset
13 <action type="shell_command">cd $INSTALL_DIR/src/ncbi-vdb</action>
15
c71031b17e08 Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents: 14
diff changeset
14 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
18
3da3d1a4deae Back to shell commands. Maybe change_directory directive does not support reading env variables?
Matt Shirley <mdshw5@gmail.com>
parents: 17
diff changeset
15 <action type="shell_command">cd $INSTALL_DIR/src/ngs/ngs-sdk</action>
15
c71031b17e08 Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents: 14
diff changeset
16 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
18
3da3d1a4deae Back to shell commands. Maybe change_directory directive does not support reading env variables?
Matt Shirley <mdshw5@gmail.com>
parents: 17
diff changeset
17 <action type="shell_command"> cd $INSTALL_DIR/src/sra-tools</action>
15
c71031b17e08 Avoid relative paths, and rename "ncbi" dir
Matt Shirley <mdshw5@gmail.com>
parents: 14
diff changeset
18 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
19 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
17
a8261e9cbe13 Add install directory to PATH.
Matt Shirley <mdshw5@gmail.com>
parents: 16
diff changeset
20 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
21 </actions>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
22 </install>
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
23 <readme>
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
24 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
25 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
26 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
27 download of a large SRA data set.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
28
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
29 Build Requirements:
11
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
30 - make
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
31 - git
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
32 - gcc
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
33 - g++
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
34 - libxml2
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
35 - libcurl4
91558de676f4 Update to latest toolkit version - fix installation issues.
Matt Shirley <mdshw5@gmail.com>
parents: 10
diff changeset
36 - zlib
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
37
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
38 On a debian based Linux OS use:
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
39
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
40 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
41
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
42 </readme>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
43 </package>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
44 </tool_dependency>