Mercurial > repos > lomereiter > sambamba_filter
comparison tool_dependencies.xml @ 2:930c9fd5eeab
Updated to version 0.3.3 of sambamba, allow use of managed dependency system, cleaned up options to simplify use.
author | lparsons |
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date | Wed, 24 Jul 2013 13:32:24 -0400 |
parents | |
children | 123168c85390 |
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1:806b3253c996 | 2:930c9fd5eeab |
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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> |