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Port details
fermi-lite Library and tool for assembling Illumina short reads in small regions
0.1.13 biology on this many watch lists=2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.13Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (8 items)
Collapse this list.
  1. bin/fml-asm
  2. include/fml.h
  3. lib/libfml.a
  4. lib/libfml.so
  5. @ldconfig
  6. /usr/local/share/licenses/fermi-lite-0.1.13/catalog.mk
  7. /usr/local/share/licenses/fermi-lite-0.1.13/LICENSE
  8. /usr/local/share/licenses/fermi-lite-0.1.13/MIT
Collapse this list.
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):
fermi-lite
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-0.1.13--0.1.13---
FreeBSD:13:quarterly-0.1.13--0.1.13---
FreeBSD:14:latest-0.1.13--0.1.13---
FreeBSD:14:quarterly-0.1.13--0.1.13---
FreeBSD:15:latest-0.1.13n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.4.1 : devel/gmake
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/lh3/fermi-lite/tar.gz/v0.1-13-g85f159e?dummy=/
Collapse this list.

Number of commits found: 4

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.1.13
28 Oct 2024 12:41:48
commit hash: 9ecc74ab460e4ad157885c16661871b58cc98352commit hash: 9ecc74ab460e4ad157885c16661871b58cc98352commit hash: 9ecc74ab460e4ad157885c16661871b58cc98352commit hash: 9ecc74ab460e4ad157885c16661871b58cc98352 files touched by this commit		 Robert Clausecker (fuz) search for other commits by this committer 
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
commit hash: b586d676edd9d0b8ac8c9b319cdbe1cda7bb2faccommit hash: b586d676edd9d0b8ac8c9b319cdbe1cda7bb2faccommit hash: b586d676edd9d0b8ac8c9b319cdbe1cda7bb2faccommit hash: b586d676edd9d0b8ac8c9b319cdbe1cda7bb2fac files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/fermi-lite: Add ONLY_FOR_ARCHS line

Reported by:	fallout
0.1.13
13 Aug 2024 09:40:45
commit hash: 80a04a9595dbc933e8acf3413ca4cc30a1260580commit hash: 80a04a9595dbc933e8acf3413ca4cc30a1260580commit hash: 80a04a9595dbc933e8acf3413ca4cc30a1260580commit hash: 80a04a9595dbc933e8acf3413ca4cc30a1260580 files touched by this commit		 Piotr Kubaj (pkubaj) search for other commits by this committer 
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
commit hash: 086a436ba4517c1f068a99669a9aabc727ebf2dfcommit hash: 086a436ba4517c1f068a99669a9aabc727ebf2dfcommit hash: 086a436ba4517c1f068a99669a9aabc727ebf2dfcommit hash: 086a436ba4517c1f068a99669a9aabc727ebf2df files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/fermi-lite: New port: Library anf tool for assembling Illumina short
reads in small regions

Number of commits found: 4
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