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Port details
jalview Viewer and editor for multiple sequence alignments
2.11.2.5 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 2.11.2.5Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-02-13 09:43:01
Last Update: 2023-06-18 09:58:53
Commit Hash: 4301fdb
Also Listed In: java
License: GPLv3
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/jalview
  2. /usr/local/share/java/jalview/jalview.jar
  3. /usr/local/share/licenses/jalview-2.11.2.5/catalog.mk
  4. /usr/local/share/licenses/jalview-2.11.2.5/LICENSE
  5. /usr/local/share/licenses/jalview-2.11.2.5/GPLv3
Collapse this list.
Dependency lines:
  • jalview>0:biology/jalview
To install the port:
cd /usr/ports/biology/jalview/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/jalview
  • pkg install jalview
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: jalview
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
jalview
ABIlatestquarterly
FreeBSD:12:aarch642.07_22.11.2.5
FreeBSD:12:amd642.11.2.52.11.2.5
FreeBSD:12:armv62.07_2-
FreeBSD:12:armv72.07_2-
FreeBSD:12:i3862.11.2.52.11.2.5
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-2.07_3
FreeBSD:13:aarch642.11.2.52.11.2.5
FreeBSD:13:amd642.11.2.52.11.2.5
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3862.11.2.52.11.2.5
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-2.11.2.5
FreeBSD:13:riscv64--
FreeBSD:14:aarch642.11.2.5-
FreeBSD:14:amd642.11.2.5-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862.11.2.5-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
FreeBSD:14:riscv64--
FreeBSD:15:amd642.11.2.5-
FreeBSD:15:armv6--
FreeBSD:15:armv7--
FreeBSD:15:i3862.11.2.5-
FreeBSD:15:mips64--
FreeBSD:15:powerpc64--
FreeBSD:15:riscv64--
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gradle761 : devel/gradle761
  2. java : java/openjdk11
Runtime dependencies:
  1. java : java/openjdk11
There are no ports dependent upon this port

Configuration Options:
Options name:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://www.jalview.org/source/
Collapse this list.

Number of commits found: 28

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.11.2.5
18 Jun 2023 09:58:53
commit hash:4301fdb6560833e91ec4fd4b50cccee532fddb01commit hash:4301fdb6560833e91ec4fd4b50cccee532fddb01commit hash:4301fdb6560833e91ec4fd4b50cccee532fddb01commit hash:4301fdb6560833e91ec4fd4b50cccee532fddb01 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1

The gradle upgrade seems to have broken jalview.

Reported by:	fallout
2.11.2.5
12 Oct 2022 06:58:18
commit hash:3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158commit hash:3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158commit hash:3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158commit hash:3a7900f35ad1dd7d0b4d152e66e9e357c7b2c158 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Update 2.11.1.4 -> 2.11.2.5
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)
2.11.1.4
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)
2.11.1.4
20 Jul 2022 14:20:57
commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.11.1.4
30 Sep 2021 21:23:30
commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
cleanup: drop support for EOL FreeBSD 11.X

Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index
2.11.1.4
27 Jun 2021 09:30:39
commit hash:389294d2b118284d007bf6a6df9b2530e4d6348acommit hash:389294d2b118284d007bf6a6df9b2530e4d6348acommit hash:389294d2b118284d007bf6a6df9b2530e4d6348acommit hash:389294d2b118284d007bf6a6df9b2530e4d6348a files touched by this commit
Guangyuan Yang (ygy) search for other commits by this committer
biology/jalview: Fix build

When switching the build dependency from devel/gradle to devel/gradle6,
the build is accidentally broken. This attempts to revert part of the
change and fix build.

Fixes:		55044a2200a4c42b6b653349f0a65dfca3f96f36
Approved by:	lwhsu (mentor, implicit), portmgr (fix build)
2.11.1.4
27 Jun 2021 01:51:07
commit hash:55044a2200a4c42b6b653349f0a65dfca3f96f36commit hash:55044a2200a4c42b6b653349f0a65dfca3f96f36commit hash:55044a2200a4c42b6b653349f0a65dfca3f96f36commit hash:55044a2200a4c42b6b653349f0a65dfca3f96f36 files touched by this commit
Guangyuan Yang (ygy) search for other commits by this committer
devel/gradle6: New port

devel/gradle needs to be updated to 7.x, while some ports build failed
under the newer version, including:

- biology/jalview
- biology/igv

Updated them to use this devel/gradle6 until they officially support 7.x.
No functional changes for these ports.

Approved by:	lwhsu (mentor)
2.11.1.4
05 Jun 2021 18:53:07
commit hash:8b8c1272ea64f9db05d8b5cfed709881429df479commit hash:8b8c1272ea64f9db05d8b5cfed709881429df479commit hash:8b8c1272ea64f9db05d8b5cfed709881429df479commit hash:8b8c1272ea64f9db05d8b5cfed709881429df479 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Broken on 11

Also fix number of lines in pkg-descr, and replace space with tab.

Reported by:	fallout
2.11.1.4
01 May 2021 17:55:55
commit hash:6707a3c942b51ab3e3cf110383e3119dfe2e49b0commit hash:6707a3c942b51ab3e3cf110383e3119dfe2e49b0commit hash:6707a3c942b51ab3e3cf110383e3119dfe2e49b0commit hash:6707a3c942b51ab3e3cf110383e3119dfe2e49b0 files touched by this commit
Tobias Kortkamp (tobik) search for other commits by this committer
Clean up some things

- Fix typos
- Remove duplicate variables
- Remove nop variables
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan
2.11.1.4
25 Apr 2021 23:00:36
commit hash:af49fbec4f0f6453b4b3dfe522107ed2918ae8f7commit hash:af49fbec4f0f6453b4b3dfe522107ed2918ae8f7commit hash:af49fbec4f0f6453b4b3dfe522107ed2918ae8f7commit hash:af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/jalview: Update 2.07 -> 2.11.1.4

Take maintainership.
2.07_3
06 Apr 2021 14:31:13
commit hash:135fdeebb99c3569e42d8162b265e15d29bd937dcommit hash:135fdeebb99c3569e42d8162b265e15d29bd937dcommit hash:135fdeebb99c3569e42d8162b265e15d29bd937dcommit hash:135fdeebb99c3569e42d8162b265e15d29bd937d files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
all: Remove all other $FreeBSD keywords.
2.07_3
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.
2.07_3
26 Dec 2020 23:01:20
Revision:559318Original commit files touched by this commit
glewis search for other commits by this committer
Restrict to Java 8, since this doesn't compile with Java 11

PR:			251774
2.07_3
26 Nov 2019 21:46:13
Revision:518482Original commit files touched by this commit
jkim search for other commits by this committer
Clean up after java/openjdk6 and java/openjdk6-jre removal

java/openjdk6 support was removed from Mk/bsd.java.mk (r512662) and
java/openjdk6 and java/openjdk6-jre were removed from the ports tree
(r512663).  Now this patch completely removes remaining stuff from the
ports tree.

PR:			241953 (exp-run)
Reviewed by:		glewis
Approved by:		portmgr (antoine)
Differential Revision:	https://reviews.freebsd.org/D22342
2.07_2
19 May 2016 10:21:25
Revision:415498Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
2.07_2
22 May 2015 13:34:22
Revision:387021Original commit files touched by this commit
mat search for other commits by this committer
Remove $FreeBSD$ from patches files in categories a-j.

With hat:	portmgr
Sponsored by:	Absolight
2.07_2
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
2.07_2
21 Jan 2014 23:18:05
Revision:340671Original commit files touched by this commit
bapt search for other commits by this committer
Fix properties on pkg-plist
2.07_2
20 Jan 2014 23:10:11
Revision:340487Original commit files touched by this commit
bapt search for other commits by this committer
Support stage
2.07_2
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
2.07_2
10 Dec 2012 11:25:28
Revision:308600Original commit files touched by this commit
bapt search for other commits by this committer
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA=	1.5+ (part1)
2.07_2
01 Oct 2012 14:45:17
Revision:305130Original commit files touched by this commit
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
2.07_2
21 Jul 2011 05:03:02
Original commit files touched by this commit
linimon search for other commits by this committer
Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,
remove support for them from bsd.java.mk.  As Jikes is not available in Java 1.5
or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports
which used it (only occurences were USE_JIKES=no).  Support for the Blackdown VM
is also removed, as it is not available in Java 1.5 and higher.

Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect
old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5.
While here, replace static values of JAVA_VERSION in files/*.in by
%%JAVA_VERSION%% .

PR:             ports/158969
Submitted by:   rene
Tested on:      pointyhat-west -exp
2.07_2
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
2.07_2
06 Jun 2008 13:08:29
Original commit files touched by this commit
edwin search for other commits by this committer
Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)
2.07_1
19 May 2007 20:32:57
Original commit files touched by this commit
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
2.07
13 Feb 2006 09:42:13
Original commit files touched by this commit
hq search for other commits by this committer
Jalview is a multiple alignment editor written in Java. It is used widely in a
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.

WWW: http://www.jalview.org

PR:             93054
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

Number of commits found: 28