biology/preseq 3.2.0 FreeBSD
Predict yield of distinct reads from a genomic library
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv3
- Categories
- biology
- Package size
- 275.5 KiB, 1492.6 KiB installed
Description
The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/preseq | 3.2.0 |
| DragonFly | biology/preseq | 3.2.0 |
Install
Binary package:
pkg install preseqFrom the ports tree:
cd /usr/ports/biology/preseq/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= preseq>0:biology/preseqPackages
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 | 3.2.0 | 3.2.0 | - | - | - |
| FreeBSD:14:quarterly | 3.2.0 | 3.2.0 | n/a | - | - |
| FreeBSD:15:latest | 3.2.0 | 3.2.0 | n/a | - | - |
| FreeBSD:15:quarterly | 3.2.0 | 3.2.0 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.2.0 | 3.2.0 | 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
libhts.so: biology/htslib
The full lists below include those, and their dependencies in turn.
Build dependencies 12
Run dependencies 12
No port depends on this one.
Configuration
No options to configure.
- USES
- localbase
- Service scripts
- none
Message after installing
===> NOTICE: The preseq port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing
Files
pkg-plist 17
- bin/preseq
- bin/to-mr
- include/GenomicRegion.hpp
- include/MappedRead.hpp
- include/OptionParser.hpp
- include/QualityScore.hpp
- include/bisulfite_utils.hpp
- include/chromosome_utils.hpp
- include/cigar_utils.hpp
- include/dna_four_bit.hpp
- include/htslib_wrapper_deprecated.hpp
- include/sam_record.hpp
- include/sim_utils.hpp
- include/smithlab_os.hpp
- include/smithlab_utils.hpp
- include/zlib_wrapper.hpp
- lib/libsmithlab_cpp.a
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| preseq-3.2.0.tar.gz | 6.488708e+06 | 95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9 |
Master sites 1
- https://github.com/smithlabcode/preseq/releases/download/v3.2.0/