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Port details
p5-Bio-Das Client-side library for Distributed Genome Annotation System
1.17_4 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 1.17_4Version of this port present on the latest quarterly branch.
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2005-09-01 13:10:39
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: perl5
License: ART10 GPLv1+
WWW:
https://metacpan.org/release/Bio-Das
Description:
Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:) DAS servers are sup- ported. (To run SSL, you will need IO::Socket::SSL and Net::SSLeay installed).
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (59 items)
Collapse this list.
  1. /usr/local/share/licenses/p5-Bio-Das-1.17_4/catalog.mk
  2. /usr/local/share/licenses/p5-Bio-Das-1.17_4/LICENSE
  3. /usr/local/share/licenses/p5-Bio-Das-1.17_4/ART10
  4. /usr/local/share/licenses/p5-Bio-Das-1.17_4/GPLv1+
  5. lib/perl5/site_perl/Bio/Das.pm
  6. lib/perl5/site_perl/Bio/Das/DSN.pm
  7. lib/perl5/site_perl/Bio/Das/Request.pm
  8. lib/perl5/site_perl/Bio/Das/Stylesheet.pm
  9. lib/perl5/site_perl/Bio/Das/Map.pm
  10. lib/perl5/site_perl/Bio/Das/FeatureIterator.pm
  11. lib/perl5/site_perl/Bio/Das/Segment.pm
  12. lib/perl5/site_perl/Bio/Das/Type.pm
  13. lib/perl5/site_perl/Bio/Das/Feature.pm
  14. lib/perl5/site_perl/Bio/Das/TypeHandler.pm
  15. lib/perl5/site_perl/Bio/Das/Util.pm
  16. lib/perl5/site_perl/Bio/Das/Request/Sequences.pm
  17. lib/perl5/site_perl/Bio/Das/Request/Dnas.pm
  18. lib/perl5/site_perl/Bio/Das/Request/Types.pm
  19. lib/perl5/site_perl/Bio/Das/Request/Feature2Segments.pm
  20. lib/perl5/site_perl/Bio/Das/Request/Features.pm
  21. lib/perl5/site_perl/Bio/Das/Request/Dsn.pm
  22. lib/perl5/site_perl/Bio/Das/Request/Entry_points.pm
  23. lib/perl5/site_perl/Bio/Das/Request/Stylesheet.pm
  24. lib/perl5/site_perl/Bio/Das/AGPServer/SQLStorage.pm
  25. lib/perl5/site_perl/Bio/Das/AGPServer/Proxy.pm
  26. lib/perl5/site_perl/Bio/Das/AGPServer/Parser.pm
  27. lib/perl5/site_perl/Bio/Das/AGPServer/Daemon.pm
  28. lib/perl5/site_perl/Bio/Das/AGPServer/Config.pm
  29. lib/perl5/site_perl/Bio/Das/AGPServer/SQLStorage/CSV/DB.pm
  30. lib/perl5/site_perl/Bio/Das/AGPServer/SQLStorage/MySQL/DB.pm
  31. lib/perl5/site_perl/Bio/Das/HTTP/Fetch.pm
  32. lib/perl5/site_perl/man/man3/Bio::Das.3.gz
  33. lib/perl5/site_perl/man/man3/Bio::Das::AGPServer::Config.3.gz
  34. lib/perl5/site_perl/man/man3/Bio::Das::AGPServer::Daemon.3.gz
  35. lib/perl5/site_perl/man/man3/Bio::Das::AGPServer::Parser.3.gz
  36. lib/perl5/site_perl/man/man3/Bio::Das::AGPServer::SQLStorage.3.gz
  37. lib/perl5/site_perl/man/man3/Bio::Das::AGPServer::SQLStorage::CSV::DB.3.gz
  38. lib/perl5/site_perl/man/man3/Bio::Das::AGPServer::SQLStorage::MySQL::DB.3.gz
  39. lib/perl5/site_perl/man/man3/Bio::Das::DSN.3.gz
  40. lib/perl5/site_perl/man/man3/Bio::Das::Feature.3.gz
  41. lib/perl5/site_perl/man/man3/Bio::Das::FeatureIterator.3.gz
  42. lib/perl5/site_perl/man/man3/Bio::Das::HTTP::Fetch.3.gz
  43. lib/perl5/site_perl/man/man3/Bio::Das::Map.3.gz
  44. lib/perl5/site_perl/man/man3/Bio::Das::Request.3.gz
  45. lib/perl5/site_perl/man/man3/Bio::Das::Request::Dnas.3.gz
  46. lib/perl5/site_perl/man/man3/Bio::Das::Request::Dsn.3.gz
  47. lib/perl5/site_perl/man/man3/Bio::Das::Request::Entry_points.3.gz
  48. lib/perl5/site_perl/man/man3/Bio::Das::Request::Feature2Segments.3.gz
  49. lib/perl5/site_perl/man/man3/Bio::Das::Request::Sequences.3.gz
  50. lib/perl5/site_perl/man/man3/Bio::Das::Request::Stylesheet.3.gz
  51. lib/perl5/site_perl/man/man3/Bio::Das::Request::Types.3.gz
  52. lib/perl5/site_perl/man/man3/Bio::Das::Segment.3.gz
  53. lib/perl5/site_perl/man/man3/Bio::Das::Stylesheet.3.gz
  54. lib/perl5/site_perl/man/man3/Bio::Das::Type.3.gz
  55. lib/perl5/site_perl/man/man3/Bio::Das::TypeHandler.3.gz
  56. lib/perl5/site_perl/man/man3/Bio::Das::Util.3.gz
  57. @owner
  58. @group
  59. @mode
Collapse this list.
Dependency lines:
  • p5-Bio-Das>0:biology/p5-Bio-Das
To install the port:
cd /usr/ports/biology/p5-Bio-Das/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/p5-Bio-Das
  • pkg install p5-Bio-Das
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: p5-Bio-Das
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (Bio-Das-1.17.tar.gz) = cfe4980e47021e69ae3ba26c88dde29aef10f934f5ca10e9ffd1a99b472792f7 SIZE (Bio-Das-1.17.tar.gz) = 105270

Packages (timestamps in pop-ups are UTC):
p5-Bio-Das
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.17_41.17_41.17_41.17_41.17_4-1.17_4-
FreeBSD:13:quarterly1.17_41.17_41.17_41.17_41.17_41.17_41.17_41.17_4
FreeBSD:14:latest1.17_41.17_41.17_41.17_41.17_41.17_4-1.17_4
FreeBSD:14:quarterly1.17_41.17_4-1.17_41.17_41.17_41.17_41.17_4
FreeBSD:15:latest1.17_41.17_4n/a1.17_4n/a1.17_41.17_41.17_4
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-BioPerl>=0 : biology/p5-BioPerl
  2. p5-HTML-Parser>=3 : www/p5-HTML-Parser
  3. p5-libwww>=5 : www/p5-libwww
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
  5. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. p5-BioPerl>=0 : biology/p5-BioPerl
  2. p5-HTML-Parser>=3 : www/p5-HTML-Parser
  3. p5-libwww>=5 : www/p5-libwww
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_p5-Bio-Das
USES:
perl5
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (12 items)
Collapse this list.
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/Bio/
  2. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/
  3. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Bio/
  4. ftp://ftp.funet.fi/pub/languages/perl/CPAN/modules/by-module/Bio/
  5. ftp://ftp.kddlabs.co.jp/lang/perl/CPAN/modules/by-module/Bio/
  6. ftp://ftp.mirrorservice.org/sites/cpan.perl.org/CPAN/modules/by-module/Bio/
  7. http://backpan.perl.org/modules/by-module/Bio/
  8. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/Bio/
  9. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/Bio/
  10. https://cpan.metacpan.org/modules/by-module/
  11. https://cpan.metacpan.org/modules/by-module/Bio/
  12. https://www.cpan.org/modules/by-module/Bio/
Collapse this list.

Number of commits found: 47

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)
1.17_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)
1.17_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)
1.17_4
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.
1.17_4
06 Oct 2018 13:06:45
Revision:481365Original commit files touched by this commit
des search for other commits by this committer
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
for where it resulted in a change in output from build-depends-list or
run-depends-list.

Approved by:	portmgr (adamw)
1.17_4
27 May 2018 20:15:20
Revision:470993Original commit files touched by this commit
sunpoet search for other commits by this committer
Update WWW

search.cpan.org is shutting down.
It will redirect to metacpan.org after June 25, 2018.

With hat:	perl
1.17_4
15 Sep 2017 08:58:50
Revision:449893Original commit files touched by this commit
mat search for other commits by this committer
Fix license information for portgs that use "the same license as Perl".

Sponsored by:	Absolight
1.17_4
18 Dec 2016 15:25:18
Revision:428870Original commit files touched by this commit
sunpoet search for other commits by this committer
- Add LICENSE
- Add NO_ARCH
- Sort *_DEPENDS
- Bump PORTREVISION for biology/p5-bioperl renaming
1.17_3
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
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
1.17_3
26 Nov 2014 13:08:38
Revision:373448Original commit files touched by this commit
mat search for other commits by this committer
Change the way Perl modules are installed, update the default Perl to 5.18.

Before, we had:

  site_perl :           lib/perl5/site_perl/5.18
  site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
  perl_man3 :           lib/perl5/5.18/man/man3

Now we have:

  site_perl : lib/perl5/site_perl
  site_arch : lib/perl5/site_perl/mach/5.18
  perl_man3 : lib/perl5/site_perl/man/man3

Modules without any .so will be installed at the same place regardless of the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.17_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
1.17_2
05 Jan 2014 12:07:21
Revision:338751Original commit files touched by this commit
az search for other commits by this committer
- support stage
1.17_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)
1.17_2
02 Aug 2013 18:52:11
Revision:324174Original commit files touched by this commit
mat search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
- Remove MAKE_JOBS_SAFE=yes, it's the default.
1.17_2
17 Dec 2012 15:39:36
Revision:309105Original commit files touched by this commit
az search for other commits by this committer
Cleanup supporting perl version 5.8 and 5.10,
lang/perl5.8 and lang/5.10 will be removed from ports tree soon.
1.17_2
10 Jun 2012 18:42:48
Original commit files touched by this commit
swills search for other commits by this committer
- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or
  RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned
  about for a while.

PR:             ports/168208
Approved by:    portmgr (miwi)
1.17_2
01 Jun 2012 05:26:28
Original commit files touched by this commit
dinoex search for other commits by this committer
- update png to 1.5.10
1.17_1
13 Mar 2012 16:15:36
Original commit files touched by this commit
pgollucci search for other commits by this committer
- Revert ports/165605 as requested by portmgr@

Note: devel/p5-B-Size and devel/p5-Devel-Arena
where intentionally not restored.

PR:             ports/165605
Approved by:    portmgr (bapt)
Feature safe:   yes (I sure hope so)
1.17_1
08 Mar 2012 18:45:38
Original commit files touched by this commit
pgollucci search for other commits by this committer
- Remove ports that only work with < perl 5.12 (devel/p5-B-Size,
devel/p5-Devel-Arena)
- Remove conditionals for PERL_LEVEL < 501200
- Remove regression-test targets b/c this will be centralized in Mk/bsd.perl.mk
- Other minor cleanups
  RUN_DEPENDS = ${BUILD_DEPENDS} -> RUN_DEPENDS:= ${BUILD_DEPENDS}

PR:             ports/165605
Submitted by:   pgollucci (myself)
Approved by:    portmgr (linimon)
Exp Run by:     linimon
Tested by:      make index
1.17_1
22 Oct 2011 23:50:23
Original commit files touched by this commit
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
1.17_1
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
1.17_1
21 Sep 2010 07:56:43
Original commit files touched by this commit Sanity Test Failure
mm search for other commits by this committer
Change dependency on old p5-Compress-Zlib, p5-IO-Compress-Base,
p5-IO-Compress-Zlib and p5-IO-Compress-Bzip2 modules to p5-IO-Compress.
Explicitly depend on p5-IO-Compress only if PERL_LEVEL < 500903
Bump PORTREVISION
1.17
30 Jun 2010 07:36:25
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.17

Feature safe:   yes
1.16
24 Jun 2010 00:24:22
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.16

Feature safe:   yes
1.15
12 Jun 2010 06:18:36
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.15
1.14_2
28 Mar 2010 06:47:48
Original commit files touched by this commit
dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
1.14_1
05 Feb 2010 11:46:55
Original commit files touched by this commit
dinoex search for other commits by this committer
- update to jpeg-8
1.14
08 Sep 2009 12:08:12
Original commit files touched by this commit
jadawin search for other commits by this committer
- Update to 1.14
1.12
27 Aug 2009 20:34:58
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.12

PR:             138230
Submitted by:   Wen Heping <wenheping@gmail.com>
1.11_1
31 Jul 2009 13:57:52
Original commit files touched by this commit
dinoex search for other commits by this committer
- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin
1.11
22 Jul 2009 16:27:08
Original commit files touched by this commit
pgollucci search for other commits by this committer
- lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks

PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)
1.11
08 Jun 2009 09:30:07
Original commit files touched by this commit
jadawin search for other commits by this committer
- Update to 1.11
1.10
11 Dec 2008 05:19:13
Original commit files touched by this commit
leeym search for other commits by this committer
- update to 1.10
1.09
31 May 2008 13:46:14
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.09
1.08
23 May 2008 12:22:21
Original commit files touched by this commit
mat search for other commits by this committer
Update to 1.08
1.07
19 May 2008 13:12:08
Original commit files touched by this commit
araujo search for other commits by this committer
- Include some ports in perl5 category.

PR:             ports/123530
Submitted by:   Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:    araujo (myself)
Approved by:    flz (portmgr)
1.07
17 Apr 2008 14:30:31
Original commit files touched by this commit
araujo search for other commits by this committer
- Take advantage of CPAN macro from bsd.sites.mk, change
${MASTER_SITE_PERL_CPAN} to CPAN.

PR:             ports/122674
Submitted by:   Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:    araujo (myself)
Approved by:    portmgr (pav)
1.07
12 Mar 2008 12:24:10
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.07
1.06
07 Sep 2007 14:45:12
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.06
- Remove 4.X cruft
1.03_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}.
1.03
14 Mar 2007 08:18:21
Original commit files touched by this commit
linimon search for other commits by this committer
Reset razi@genet.sickkids.on.ca due to maintainer-timeouts and no response to
email.

Hat:            portmgr
1.03
19 Dec 2006 06:47:45
Original commit files touched by this commit
rafan search for other commits by this committer
- Update to 1.03

PR:             ports/106300
Submitted by:   chinsan
Approved by:    maintainer timeout (15 days)
1.02
03 Dec 2006 12:45:59
Original commit files touched by this commit
demon search for other commits by this committer
Correct path to Compress::Zlib.pm after recent p5-Compress-Zlib update.
1.02
22 Jan 2006 08:20:34
Original commit files touched by this commit
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
1.02
05 Jan 2006 22:31:12
Original commit files touched by this commit
pav search for other commits by this committer
- Remove symlinks that belong to mtree

Approved by:    maintainers
1.02
26 Nov 2005 03:40:59
Original commit files touched by this commit
fenner search for other commits by this committer
Add the right MASTER_SITE_SUBDIR, so that this port is fetchable from
 20 sites instead of just 1.
1.02
01 Sep 2005 13:09:33
Original commit files touched by this commit
garga search for other commits by this committer
Add p5-Bio-Das 1.02, client-side library for Distributed Genome
Annotation System.

PR:             ports/76379
Submitted by:   Razi Khaja <razi@genet.sickkids.on.ca>

Number of commits found: 47