| Port details |
- infernal Search sequence databases for structural RNA homologs
- 1.1.4_1 biology
 =2      1.1.4_1Version of this port present on the latest quarterly branch. - Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2018-06-06 15:15:35
- Last Update: 2024-02-22 13:23:47
- Commit Hash: 806984b
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSD3CLAUSE
- WWW:
- http://eddylab.org/infernal/
- Description:
- Infernal, standing for "INFERence of RNA ALignment", is a tool for searching
DNA sequence database for RNA structure and sequence similarities.
It is based on Covariance Model (CM), which scores a combination of sequence
consensus and RNA secondary structure consensus, and thus is more capable of
identifying RNA homologs than using primary sequence profile.
The Rfam database of RNA families is based on Infernal.
Citation:
Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches,
Bioinformatics 29: 2933-2935.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- infernal>0:biology/infernal
- To install the port:
- cd /usr/ports/biology/infernal/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/infernal
- pkg install infernal
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: infernal
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: amd64 i386 powerpc powerpc64 powerpc64le powerpcspe
- distinfo:
- TIMESTAMP = 1665487539
SHA256 (infernal-1.1.4.tar.gz) = f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc
SIZE (infernal-1.1.4.tar.gz) = 29499238
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>=4.3 : devel/gmake
- Test dependencies:
-
- python3.9 : lang/python39
- perl5>=5.36<5.37 : lang/perl5.36
- This port is required by:
- for Run
-
- biology/tRNAscan-SE
Configuration Options:- ===> The following configuration options are available for infernal-1.1.4_1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
TEST=off: Build and/or run tests
===> Use 'make config' to modify these settings
- Options name:
- biology_infernal
- USES:
- compiler:c11 gmake perl5 python:test shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
1.1.4_1
22 Feb 2024 13:23:47
 |
Muhammad Moinur Rahman (bofh) |
biology/infernal: Moved man to share/man
Approved by: portmgr (blanket) |
1.1.4
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
1.1.4
12 Oct 2022 10:15:54
|
Nuno Teixeira (eduardo)
Author: Motomichi Matsuzaki |
biology/infernal: Update to 1.1.4
ChangeLog: http://eddylab.org/infernal/RELEASE-1.1.4.md
PR: 266967 |
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) |
1.1.3
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  ) |
1.1.3
01 Apr 2022 15:09:49
|
Dmitry Marakasov (amdmi3) |
*/*: fix trailing whitespace in pkg-descr's
Approved by: portmgr blanket |
1.1.3
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
1.1.3
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.1.3
24 Sep 2020 20:38:59
 |
linimon |
Also enable on powerpc64le.
Approved by: portmgr (tier-2 blanket) |
1.1.3
27 Jan 2020 17:57:15
|
fernape |
biology/infernal: update to 1.1.3
PR: 243247
Submitted by: mzaki@e-mail.ne.jp (maintainer) |
1.1.2
27 Sep 2018 23:02:56
|
linimon |
Allow building on powerpc64.
PR: 231759
Submitted by: Piotr Kubaj
Approved by: portmgr (tier-2 blanket) |
1.1.2
06 Jun 2018 15:15:18
|
krion |
Add new port: biology/infernal
Infernal is a tool for searching DNA sequence database for RNA
structure and sequence similarities. The Rfam database of RNA
families is based on Infernal, and we can search DNA sequences for
structural homologs of Rfam families.
WWW: http://eddylab.org/infernal/
PR: 228776
Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> |
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