Port details |
- fermi-lite Library and tool for assembling Illumina short reads in small regions
- 0.1.13 biology =2 0.1.13Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2024-08-03 08:30:10
- Last Update: 2024-10-28 12:41:48
- Commit Hash: 9ecc74a
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: devel
- License: MIT
- WWW:
- https://github.com/lh3/fermi-lite
- Description:
- Fermi-lite is a standalone C library as well as a command-line tool for
assembling Illumina short reads in regions from 100bp to 10 million bp in size.
It is largely a light-weight in-memory version of fermikit without generating
any intermediate files. It inherits the performance, the relatively small memory
footprint and the features of fermikit. In particular, fermi-lite is able to
retain heterozygous events and thus can be used to assemble diploid regions for
the purpose of variant calling. It is one of the limited choices for local
re-assembly and arguably the easiest to interface.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- fermi-lite>0:biology/fermi-lite
- To install the port:
- cd /usr/ports/biology/fermi-lite/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/fermi-lite
- pkg install fermi-lite
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: fermi-lite
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: aarch64 amd64 armv7 i386
- distinfo:
- TIMESTAMP = 1722640889
SHA256 (lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz) = eafa2f290c3857bcae4804fa3e86c59b8437777835cc601699d78e2192ca44fd
SIZE (lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz) = 248339
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.4.1 : devel/gmake
- This port is required by:
- for Run
-
- biology/gatk
Configuration Options:
- No options to configure
- Options name:
- biology_fermi-lite
- USES:
- gmake localbase
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 4
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
0.1.13 28 Oct 2024 12:41:48 |
Robert Clausecker (fuz) |
biology/fermi-lite: port to armv7/aarch64
This applies the sse2neon header on armv7 and aarch64 to implement
the SSE intrinsics.
Approved by: yuri (maintainer timeout, two weeks)
Differential Revision: https://reviews.freebsd.org/D47128 |
0.1.13 19 Sep 2024 21:05:26 |
Yuri Victorovich (yuri) |
biology/fermi-lite: Add ONLY_FOR_ARCHS line
Reported by: fallout |
0.1.13 13 Aug 2024 09:40:45 |
Piotr Kubaj (pkubaj) |
biology/fermi-lite: fix build on powerpc64le
In file included from ksw.c:28:
/usr/lib/clang/18/include/ppc_wrappers/emmintrin.h:32:2: error: "Please read
comment above. Use -DNO_WARN_X86_INTRINSICS to disable this error."
32 | #error
\
| ^
In file included from ksw.c:28:
In file included from /usr/lib/clang/18/include/ppc_wrappers/emmintrin.h:45:
/usr/lib/clang/18/include/ppc_wrappers/xmmintrin.h:31:2: error: "Please read
comment above. Use -DNO_WARN_X86_INTRINSICS to disable this error."
31 | #error
\
| ^
In file included from ksw.c:28:
In file included from /usr/lib/clang/18/include/ppc_wrappers/emmintrin.h:45:
In file included from /usr/lib/clang/18/include/ppc_wrappers/xmmintrin.h:58:
/usr/lib/clang/18/include/ppc_wrappers/mmintrin.h:31:2: error: "Please read
comment above. Use -DNO_WARN_X86_INTRINSICS to disable this error."
31 | #error
\
| ^
3 errors generated. |
0.1.13 03 Aug 2024 08:27:25 |
Yuri Victorovich (yuri) |
biology/fermi-lite: New port: Library anf tool for assembling Illumina short
reads in small regions |
Number of commits found: 4
|