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non port: biology/consed/Makefile

Number of commits found: 20

Saturday, 4 Apr 2020
20:51 antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
Original commitRevision:530719 
Wednesday, 6 Nov 2019
12:48 antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
Original commitRevision:516880 
Monday, 5 Sep 2016
19:23 tijl search for other commits by this committer
- Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with
  Mk/Uses/linux.mk.
- Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with
  USES+=linux:\1 in all ports.
- Replace USE_LINUX_APPS with USE_LINUX in all ports.
- Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some
  ports.
- When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY
  are defined.
- Remove BRANDELF_DIRS and BRANDELF_FILES handling.  In the very rare cases
  that it is still necessary ports can run ${BRANDELF} from post-patch.
- Remove AUTOMATIC_PLIST handling.  Only one port used it.
- Fix Linux MASTER_SITES.
- Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with
  default versions framework.
- bsd.port.mk:
  - Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX.
  - Put USE_LINUX_PREFIX handling after USES processing.
  - Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can
    give these variables a different default value.
  - When a package needs to run Linux ldconfig check before installation if
    Linux support is enabled.
- emulators/linux_base-*:
  - Use USES=linux and remove duplication.
  - Remove files/lp.  FreeBSD or CUPS lp(1) should work.
  - Remove files/yp.conf.  No longer seems to be used.
  - Remove pkg-deinstall and move pkg-install into pkg-plist.
  - Update pkg-descr and pkg-message.
  - Fix handling of ldconfig cache in pkg-plist.
- devel/fb-adb: Use a Linux shell to run a Linux script but patch the script
  to use FreeBSD mkdir so mkdir -p $path creates $path and not
  /compat/linux/$path.

PR:		211645
Exp-run by:	antoine
Approved by:	portmgr (antoine)
Original commitRevision:421387 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Saturday, 26 Dec 2015
13:26 rene search for other commits by this committer
biology/consed: undeprecate, it presumably builds fine but it is restricted.

Add a note to ports/LEGAL
Original commitRevision:404510 
Sunday, 25 Oct 2015
19:35 antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
Original commitRevision:400160 
Monday, 13 Apr 2015
14:49 mat search for other commits by this committer
${ENV} does not exist, it is called ${SETENV}.
Original commitRevision:383926 
Sunday, 5 Apr 2015
17:55 bapt search for other commits by this committer
Mark as broken unfetchable ports
Original commitRevision:383309 
Saturday, 23 Aug 2014
18:04 pi search for other commits by this committer
update ports:
	biology/phrab
	biology/phred
	biology/consed

Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.

PR:		191336
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
Original commitRevision:365765 
Tuesday, 29 Jul 2014
19:11 adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
Original commitRevision:363374 
Monday, 9 Jun 2014
11:21 olgeni search for other commits by this committer
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
Original commitRevision:357139 
Saturday, 10 May 2014
18:07 antoine search for other commits by this committer
Replace maintainer's email address with one that seems to work

With hat:	portmgr
Original commitRevision:353593 
Friday, 21 Feb 2014
13:35 ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
Original commitRevision:345397 
Monday, 10 Feb 2014
13:54 ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
Original commitRevision:343634 
Friday, 3 Jan 2014
15:46 adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
Original commitRevision:338550 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Saturday, 7 Sep 2013
07:44 az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
Original commitRevision:326575 
Thursday, 19 Mar 2009
17:28 bsam search for other commits by this committer
Welcome to the new linux ports infrastructure which allows using
both current (fc4) and future linux (f8) distributions at one
ports tree.

The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.

The idea was taken from bsd.gnome.mk and others.

More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.

Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.

Other changes are coming. Stay tuned!

PR:             ports/132510
Submitted by:   bsam (me)
Exp-run by:     portmgr (pav)
Original commit
Sunday, 25 May 2008
23:05 edwin search for other commits by this committer
Teach the building cluster that these ports are not to be build
Original commit
Saturday, 24 May 2008
07:00 edwin search for other commits by this committer
New port: biology/consed viewing and editing workbench for sequence
assembly

        Consed is a tool for viewing, editing, and finishing sequence
assemblies.

        The port is constituted of 4 parts:
        biology/phred: base caller with quality evaluation
        biology/phrap: sequence assembler for shotgun sequencing
        biology/consed: workbench
        biology/phd2fasta: small utility

        All these can be used separately; however, most function
        of consed depends on the others.

        Although these programs are licensed freely for academic
        and nonprofit purposes, users have to contact the authors
        to get the softwares.
        Phred (including phd2fasta) and phrap are emailed,
        and consed can be downloaded to a restricted IP address.
        For commercial users, the licensing fee is ca. $10,000 at
        the time of writing.

PR:             ports/118548
Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Original commit

Number of commits found: 20