annotate tool_dependencies.xml @ 23:b94593ba997b

Can't use concurrency.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 21:23:35 -0400
parents 4102c1600aa0
children 22d9fe442c50
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>
19
6d25dfb4dbb4 Trying this again.
Matt Shirley <mdshw5@gmail.com>
parents: 18
diff changeset
9 <action type="shell_command">
6d25dfb4dbb4 Trying this again.
Matt Shirley <mdshw5@gmail.com>
parents: 18
diff changeset
10 git clone https://github.com/mdshw5/sra-tools.git
6d25dfb4dbb4 Trying this again.
Matt Shirley <mdshw5@gmail.com>
parents: 18
diff changeset
11 git clone https://github.com/mdshw5/ncbi-vdb.git
6d25dfb4dbb4 Trying this again.
Matt Shirley <mdshw5@gmail.com>
parents: 18
diff changeset
12 git clone https://github.com/mdshw5/ngs.git
6d25dfb4dbb4 Trying this again.
Matt Shirley <mdshw5@gmail.com>
parents: 18
diff changeset
13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
22
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
14 cd $INSTALL_DIR/src/ncbi-vdb
21
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
23
b94593ba997b Can't use concurrency.
Matt Shirley <mdshw5@gmail.com>
parents: 22
diff changeset
16 make
21
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
17 make install
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
18 cd $INSTALL_DIR/ngs/ngs-sdk
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
23
b94593ba997b Can't use concurrency.
Matt Shirley <mdshw5@gmail.com>
parents: 22
diff changeset
20 make
21
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
21 make install
22
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
22 cd $INSTALL_DIR/src/sra-tools
21
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
23 ./configure --prefix=$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
23
b94593ba997b Can't use concurrency.
Matt Shirley <mdshw5@gmail.com>
parents: 22
diff changeset
24 make
21
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
25 make install
847db227d9ce OK now.
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
26 sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/lib64/ncbi/default.kfg
19
6d25dfb4dbb4 Trying this again.
Matt Shirley <mdshw5@gmail.com>
parents: 18
diff changeset
27 </action>
17
a8261e9cbe13 Add install directory to PATH.
Matt Shirley <mdshw5@gmail.com>
parents: 16
diff changeset
28 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
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>