BSD Portsbiology/bamtools 2.5.3 FreeBSD
API and toolkit for handling BAM files
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MIT
- Categories
- biology
- Package size
- 319.9 KiB, 1052.7 KiB installed
Description
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. BAM is the binary alternative to the sequence alignment/map (SAM) format used for storing genetic sequence data. It uses BGZF block compression implemented on top of the standard gzip file format to provide good compression while allowing efficient random access for indexed queries.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/bamtools | 2.5.3 |
| DragonFly | biology/bamtools | 2.5.2_2 |
Install
Binary package:
pkg install bamtoolsFrom the ports tree:
cd /usr/ports/biology/bamtools/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= bamtools>0:biology/bamtools
LIB_DEPENDS= libbamtools.so:biology/bamtoolsPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.5.3 | 2.5.3 | 2.5.2_1 | 2.5.3 | 2.5.3 |
| FreeBSD:14:quarterly | 2.5.3 | 2.5.3 | n/a | 2.5.3 | 2.5.3 |
| FreeBSD:15:latest | 2.5.3 | 2.5.3 | n/a | 2.5.3 | 2.5.3 |
| FreeBSD:15:quarterly | 2.5.3 | 2.5.3 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.5.3 | 2.5.3 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 1
libjsoncpp.so: devel/jsoncpp
The full lists below include those, and their dependencies in turn.
Build dependencies 15
Run dependencies 1
Required by 2
Configuration
No options to configure.
- USES
- cmake
- Service scripts
- none
Files
pkg-plist 25
- bin/bamtools
- include/bamtools/api/BamAlgorithms.h
- include/bamtools/api/BamAlignment.h
- include/bamtools/api/BamAux.h
- include/bamtools/api/BamConstants.h
- include/bamtools/api/BamIndex.h
- include/bamtools/api/BamMultiReader.h
- include/bamtools/api/BamReader.h
- include/bamtools/api/BamWriter.h
- include/bamtools/api/IBamIODevice.h
- include/bamtools/api/SamConstants.h
- include/bamtools/api/SamHeader.h
- include/bamtools/api/SamProgram.h
- include/bamtools/api/SamProgramChain.h
- include/bamtools/api/SamReadGroup.h
- include/bamtools/api/SamReadGroupDictionary.h
- include/bamtools/api/SamSequence.h
- include/bamtools/api/SamSequenceDictionary.h
- include/bamtools/api/algorithms/Sort.h
- include/bamtools/api/api_global.h
- include/bamtools/api/bamtools_api_export.h
- include/bamtools/shared/bamtools_global.h
- lib/libbamtools.so
- lib/libbamtools.so.
- libdata/pkgconfig/bamtools-1.pc
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| pezmaster31-bamtools-v2.5.3_GH0.tar.gz | 245648 | 7d4e59bac7c03bde488fe43e533692f78b5325a097328785ec31373ffac08344 |