notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
Port details
seqwish Alignment to variation graph inducer
0.7.11 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 0.7.10Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-07-21 21:42:05
Last Update: 2024-11-16 10:27:18
Commit Hash: df5c1f3
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
License: MIT
WWW:
https://github.com/ekg/seqwish
Description:
seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when working with large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.
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 (4 items)
Collapse this list.
  1. bin/seqwish
  2. /usr/local/share/licenses/seqwish-0.7.11/catalog.mk
  3. /usr/local/share/licenses/seqwish-0.7.11/LICENSE
  4. /usr/local/share/licenses/seqwish-0.7.11/MIT
Collapse this list.
Dependency lines:
  • seqwish>0:biology/seqwish
To install the port:
cd /usr/ports/biology/seqwish/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/seqwish
  • pkg install seqwish
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: seqwish
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1731123736 SHA256 (seqwish-v0.7.11.tar.gz) = 9cbf51990787a93c58a1ee04239608785beb7e8a38efeb02929121b3c8c4a103 SIZE (seqwish-v0.7.11.tar.gz) = 12125014

Packages (timestamps in pop-ups are UTC):
seqwish
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.7.110.7.11------
FreeBSD:13:quarterly0.7.100.7.10------
FreeBSD:14:latest0.7.100.7.11------
FreeBSD:14:quarterly0.7.100.7.10------
FreeBSD:15:latest--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for seqwish-0.7.11: OPENMP=on: Parallel processing support via OpenMP ===> Use 'make config' to modify these settings
Options name:
biology_seqwish
USES:
cmake:noninja compiler:c++14-lang
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://github.com/ekg/seqwish/releases/download/v0.7.11/
Collapse this list.

Number of commits found: 8

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.7.11
16 Nov 2024 10:27:18
commit hash: df5c1f3f0986d0af4ca5d5f6357638eebf89ccfacommit hash: df5c1f3f0986d0af4ca5d5f6357638eebf89ccfacommit hash: df5c1f3f0986d0af4ca5d5f6357638eebf89ccfacommit hash: df5c1f3f0986d0af4ca5d5f6357638eebf89ccfa files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: Broken on 15 with clng-19

Reported by:	fallout
0.7.11
09 Nov 2024 06:06:06
commit hash: daf432561b9dd9f11baad8923c72cdc4c01bc12fcommit hash: daf432561b9dd9f11baad8923c72cdc4c01bc12fcommit hash: daf432561b9dd9f11baad8923c72cdc4c01bc12fcommit hash: daf432561b9dd9f11baad8923c72cdc4c01bc12f files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: update 0.7.10 → 0.7.11
0.7.10
18 May 2024 17:29:58
commit hash: 04eb409d363d507577269d3bb70496cba84b8b9dcommit hash: 04eb409d363d507577269d3bb70496cba84b8b9dcommit hash: 04eb409d363d507577269d3bb70496cba84b8b9dcommit hash: 04eb409d363d507577269d3bb70496cba84b8b9d files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: update 0.7.9 → 0.7.10
0.7.9
05 Nov 2023 23:07:52
commit hash: 25d04c675ed487d44679b27653a82501c80b4138commit hash: 25d04c675ed487d44679b27653a82501c80b4138commit hash: 25d04c675ed487d44679b27653a82501c80b4138commit hash: 25d04c675ed487d44679b27653a82501c80b4138 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: Add comment
0.7.9
25 Aug 2023 06:22:32
commit hash: 498d092add953755ff70e2fd974073fd74ae50f1commit hash: 498d092add953755ff70e2fd974073fd74ae50f1commit hash: 498d092add953755ff70e2fd974073fd74ae50f1commit hash: 498d092add953755ff70e2fd974073fd74ae50f1 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: Add comment
0.7.9
17 Aug 2023 05:27:09
commit hash: 219d517c10a165d4775af09d14fe9f850bb24863commit hash: 219d517c10a165d4775af09d14fe9f850bb24863commit hash: 219d517c10a165d4775af09d14fe9f850bb24863commit hash: 219d517c10a165d4775af09d14fe9f850bb24863 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: Broken on i386

Reported by:	fallout
0.7.9
21 Jul 2023 23:47:03
commit hash: 194370068a29441d6898267de0655bc10d49d648commit hash: 194370068a29441d6898267de0655bc10d49d648commit hash: 194370068a29441d6898267de0655bc10d49d648commit hash: 194370068a29441d6898267de0655bc10d49d648 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: Correct COMMENT and WWW
0.7.9
21 Jul 2023 21:38:59
commit hash: 04d04b8dafba8cd1a9875fe8f027c1e310d8ed5fcommit hash: 04d04b8dafba8cd1a9875fe8f027c1e310d8ed5fcommit hash: 04d04b8dafba8cd1a9875fe8f027c1e310d8ed5fcommit hash: 04d04b8dafba8cd1a9875fe8f027c1e310d8ed5f files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/seqwish: New port: Assembly By Short Sequences: parallel, paired-end
sequence assembler

Number of commits found: 8