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Port details
hisat2 Alignment program for mapping next-generation sequencing reads
2.2.1_2 biology on this many watch lists=0 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 Version of this port present on the latest quarterly branch.
Maintainer: search for ports maintained by this maintainer
Port Added: 2019-01-11 16:02:24
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: perl5 python
License: GPLv3
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
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  1. /usr/local/share/licenses/hisat2-2.2.1_2/
  2. /usr/local/share/licenses/hisat2-2.2.1_2/LICENSE
  3. /usr/local/share/licenses/hisat2-2.2.1_2/GPLv3
  4. bin/hisat2
  5. bin/hisat2-align-l
  6. bin/hisat2-align-s
  7. bin/hisat2-build
  8. bin/hisat2-build-l
  9. bin/hisat2-build-s
  10. bin/hisat2-inspect
  11. bin/hisat2-inspect-l
  12. bin/hisat2-inspect-s
  13. bin/hisat2-repeat
  14. libexec/hisat2/
  15. libexec/hisat2/
  16. libexec/hisat2/
  17. libexec/hisat2/
  18. libexec/hisat2/
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  69. libexec/hisat2/
  70. @owner
  71. @group
  72. @mode
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Dependency lines:
  • hisat2>0:biology/hisat2
To install the port:
cd /usr/ports/biology/hisat2/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/hisat2
  • pkg install hisat2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: hisat2
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le riscv64

Packages (timestamps in pop-ups are UTC):
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. simde>0 : devel/simde
  2. gmake>=4.3 : devel/gmake
  3. python3.9 : lang/python39
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/rna-seq

Configuration Options:
Options name:
FreshPorts was unable to extract/find any pkg message
Master Sites:
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Number of commits found: 9

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
16 Dec 2021 21:38:56
commit hash:e404b5546c3d97c68066d31fd1370a17c7680fdacommit hash:e404b5546c3d97c68066d31fd1370a17c7680fdacommit hash:e404b5546c3d97c68066d31fd1370a17c7680fdacommit hash:e404b5546c3d97c68066d31fd1370a17c7680fda files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hisat2: enable on riscv64
28 Nov 2021 22:52:09
commit hash:6863162eb9e7e3c3acdf4365f3dd7d5ea0279234commit hash:6863162eb9e7e3c3acdf4365f3dd7d5ea0279234commit hash:6863162eb9e7e3c3acdf4365f3dd7d5ea0279234commit hash:6863162eb9e7e3c3acdf4365f3dd7d5ea0279234 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/hisat2: Add support for powerpc64* and aarch64

Minor patches to utilize simde to emulate SSE (from Debian package)
Add -fsigned-char since clang defaults to unsigned on aarch64
Remove -DPOPCNT_CAPABILITY (not truly safe even on amd64)
27 Nov 2021 13:26:45
commit hash:5ed416aa0967ac4cf5153f9f7cae4b9f14c56966commit hash:5ed416aa0967ac4cf5153f9f7cae4b9f14c56966commit hash:5ed416aa0967ac4cf5153f9f7cae4b9f14c56966commit hash:5ed416aa0967ac4cf5153f9f7cae4b9f14c56966 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/hisat2: Remove patch causing quality scores of "-0"
26 Nov 2021 22:05:43
commit hash:d8bc1eb7963a6f62b707404af33e0256ac2f6d99commit hash:d8bc1eb7963a6f62b707404af33e0256ac2f6d99commit hash:d8bc1eb7963a6f62b707404af33e0256ac2f6d99commit hash:d8bc1eb7963a6f62b707404af33e0256ac2f6d99 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/hisat2: Update to 2.2.1

07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
11 Jan 2019 16:02:05
Revision:489981Original commit files touched by this commit
jwb search for other commits by this committer
New port: biology/hisat2: Program for mapping next-generation sequencing reads

Approved by:    jrm (mentor, implicit)

Number of commits found: 9