Mercurial > repos > matt-shirley > ncbi_sra_toolkit

annotate tool_dependencies.xml @ 7:e724bff23fb6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Bump SRA toolkit version
author Matt Shirley <mdshw5@gmail.com>
date Thu, 13 Mar 2014 16:08:12 -0400
parents 293927a46697
children 16f96ab0196b
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>
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
3 <package name="sra_toolkit" version="2.3.4-2">
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>
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
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>
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
7 <action type="shell_command">make release</action>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
8 <action type="shell_command">make static</action>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
9 <action type="shell_command">make</action>
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
10 <action type="make_directory">$INSTALL_DIR/bin</action>
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
11 <action type="make_directory">$INSTALL_DIR/ncbi</action>
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
12 <action type="make_directory">$INSTALL_DIR/ncbi/public</action>
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
13 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
14 <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
15 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
16 </actions>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
17 </install>
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
18 <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
19 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
20 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
21 download of a large SRA data set.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
22
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
23 Build Requirements:
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
24 ar
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
25 bash
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
26 make
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
27 gcc, g++
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
28 libxml2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
29 libcurl4
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
30 zlib
7
e724bff23fb6 Bump SRA toolkit version
Matt Shirley <mdshw5@gmail.com>
parents: 2
diff changeset
31
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
32 On a debian based Linux OS use:
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
33
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
34 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
35 </readme>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
36 </package>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
37 </tool_dependency>