Mercurial > repos > lomereiter > sambamba_filter

comparison tool_dependencies.xml @ 2:930c9fd5eeab

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
author lparsons
date Wed, 24 Jul 2013 13:32:24 -0400
parents
children 123168c85390
comparison
equal deleted inserted replaced
1:806b3253c996 2:930c9fd5eeab
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="sambamba" version="0.3.3">
4 <install version="1.0">
5 <actions>
6 <action type="shell_command">git clone --recursive https://github.com/lomereiter/sambamba</action>
7 <action type="shell_command">git checkout v0.3.3</action>
8 <action type="shell_command">git submodule update --recursive</action>
9 <action type="shell_command">make release</action>
10 <action type="move_directory_files">
11 <source_directory>build</source_directory>
12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
13 </action>
14 <action type="set_environment">
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
16 </action>
17 </actions>
18 </install>
19 <readme>
20 This tool uses the sambamba view command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
21
22 There are a three options for installation of sambamba:
23
24 1) Automated toolshed installation. This requires that a D2 compiler (dmd >= 2.063) is installed. The automated installation will attempt to use the dmd compiler and thus **will not be optimized**.
25
26 2) Manual compilation. For performance reasons, the sambamba developers recommend you use either GDC or LDC as they use GCC and LLVM backends and do a much better job at optimization. You should then use the sambamba-ldmd2-64 make target. See https://github.com/lomereiter/sambamba/wiki/Command-line-tools for more information.
27
28 3) Precompiled binary (recommended). You may wish to simply use a precompiled binary of sambamba available at https://www.dropbox.com/sh/v05fsb5aarob3xe/iUHgyud31a/sambamba.
29
30 If you choose option 2 or 3, sambamba may be installed as a "Managed Dependency" in Galaxy's "tool_dependency_dir". See http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies.
31
32 The development repository for the galaxy wrapper is at: https://bitbucket.org/lance_parsons/sambamba_filter_galaxy_wrapper.
33 The sambamba development repository is at: https://github.com/lomereiter/sambamba.
34 </readme>
35 </package>
36 </tool_dependency>