| Port details |
- hisat2 Alignment program for mapping next-generation sequencing reads
- 2.2.1_2 biology
 =2      2.2.1_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2019-01-11 16:02:24
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: perl5 python
- License: GPLv3
- WWW:
- https://ccb.jhu.edu/software/hisat2/index.shtml
- Description:
- HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as to a single reference genome).
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- 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
- distinfo:
- TIMESTAMP = 1637941870
SHA256 (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599
SIZE (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = 6761242
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:
-
- simde>0 : devel/simde
- gmake>=4.3 : devel/gmake
- python3.9 : lang/python39
- perl5>=5.32.r0<5.33 : lang/perl5.32
- Runtime dependencies:
-
- python3.9 : lang/python39
- perl5>=5.32.r0<5.33 : lang/perl5.32
- This port is required by:
- for Run
-
- biology/biostar-tools
- biology/rna-seq
Configuration Options:- No options to configure
- Options name:
- biology_hisat2
- USES:
- gmake localbase perl5 python shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 9
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
07 Sep 2022 21:58:51
 |
Stefan Eßer (se) |
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) |
2.2.1_2
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
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  ) |
2.2.1_2
16 Dec 2021 21:38:56
|
Piotr Kubaj (pkubaj) |
biology/hisat2: enable on riscv64 |
2.2.1_2
28 Nov 2021 22:52:09
|
Jason W. Bacon (jwb) |
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) |
2.2.1_1
27 Nov 2021 13:26:45
|
Jason W. Bacon (jwb) |
biology/hisat2: Remove patch causing quality scores of "-0" |
2.2.1
26 Nov 2021 22:05:43
|
Jason W. Bacon (jwb) |
biology/hisat2: Update to 2.2.1
Changes: https://github.com/DaehwanKimLab/hisat2/tags |
2.1.0.23
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.1.0.23
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.1.0.23
11 Jan 2019 16:02:05
 |
jwb |
New port: biology/hisat2: Program for mapping next-generation sequencing reads
Approved by: jrm (mentor, implicit) |
Number of commits found: 9
|
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