Commit Graph

158 Commits

Author SHA1 Message Date
kmos
9e314f293e Do the usual c99 dance for base-gcc to fix the build on sparc64 2022-11-28 16:07:04 +00:00
martin
c20a8bf654 Update py-biopython to 1.80. 2022-11-19 15:46:59 +00:00
sthen
81d581665c bump for MODPY_DEFAULT_VERSION_3 change 2022-11-13 15:27:35 +00:00
sthen
2206a80000 rename MODPY_PEP517 to MODPY_PYBUILD which is a bit less of a
magic-numbers name and more of a nod at the frontend we're actually
using for the build.
2022-09-13 20:56:17 +00:00
sthen
6993e89da4 missed bump 2022-09-11 12:53:08 +00:00
sthen
d5f1ddc420 use MODPY_PEP517 2022-09-10 21:52:11 +00:00
naddy
1c2ff4f353 drop RCS Ids 2022-03-11 18:22:02 +00:00
sthen
385739a94f drop rcs id in category Makefiles 2022-03-09 16:18:03 +00:00
sthen
8ad2bb9a3a bump REVISION for switch from Python 3.8 -> 3.9 2021-11-02 00:00:12 +00:00
benoit
7ba680ad9b Update to p5-Bio-DB-NCBIHelper-1.7.7. 2021-07-12 09:01:59 +00:00
martin
17931fe70d Update biopython to 1.79. 2021-06-23 10:46:49 +00:00
benoit
504b00b43a Update to bioperl-1.7.8 from wen heping 2021-02-07 14:49:43 +00:00
kn
496a7504b0 Remove biology/nutdb
It fails to build with "-fno-common" and HOMEPAGE indicates that it's
no longer being worked on.

The website points at https://cronometer.com/ (website / mobile app) to be
used in the interim until upstream's NUT rewrite is done.

There is NUTsqlite on the sourceforge site's files section, not sure
but perhaps that is the rewrite talked about on the website. It is
written in Tcl/Tk. (thanks sthen)

OK sthen
2021-01-30 14:27:32 +00:00
sthen
d80c418015 regen PLISTs for python ports with .so files that end up renamed due to
the EXT_SUFFIX change in Python 3.8.7
2021-01-04 14:06:26 +00:00
sthen
42942be5f6 add missing ,python3 for py-biopython (FLAVOR=python3) 2020-12-30 15:55:46 +00:00
martin
f397dad535 Update py-biothyon to 1.78. Take maintainer and completely overhaul the
port including the switch to python3-only.

ok kmos
2020-10-25 18:12:58 +00:00
cwen
b2711d7cec bioperl: update to 1.7.7
Beware, bioperl has been split in several submodules, please check
an exhaustive list of what it implies at:
https://metacpan.org/changes/distribution/BioPerl#L71

OK afresh1@
2020-08-25 23:56:31 +00:00
cwen
e50137b971 p5-Bio-ASN1-EntrezGene: update to 1.73
Changelog: https://metacpan.org/changes/distribution/Bio-ASN1-EntrezGene

@conflict tweak from sthen
OK afresh1@
2020-08-25 23:54:01 +00:00
cwen
42adc8887b +p5-Bio-DB-EMBL
+p5-Bio-DB-NCBIHelper
+p5-Bio-Variation
+p5-Bio-Cluster
2020-08-25 23:44:13 +00:00
cwen
08fd27b76d Import biology/p5-Bio-Cluster
This interface is the basic structure for a cluster of bioperl objects.

@conflict tweak from sthen
OK afresh1@
2020-08-25 23:43:06 +00:00
cwen
c5b918a847 Import biology/p5-Bio-Variation
Bio::Variation name space contains modules to store sequence variation
information as differences between the reference sequence and changes
sequences. Also included are classes to write out and recrete objects from
EMBL-like flat files and XML. Lastly, there are simple classes to calculate
values for sequence change objects.

@conflict tweak from sthen
OK afresh1@
2020-08-25 23:41:26 +00:00
cwen
7b48935d5a Import biology/p5-Bio-DB-NCBIHelper
This module provides a single place to setup some common methods
for querying NCBI web databases.

@conflict tweak from sthen
OK afresh1@
2020-08-25 23:39:36 +00:00
cwen
c6d6e88320 Import biology/p5-Bio-DB-EMBL
This module allows the dynamic retrieval of sequence objects
Bio::Seq from the EMBL database using the dbfetch script at EBI:
https://www.ebi.ac.uk/Tools/dbfetch/dbfetch

@conflict tweak from sthen
OK afresh1@
2020-08-25 23:37:52 +00:00
sthen
95d31a4bd8 bump for search.cpan.org->metacpan.org change 2020-07-03 21:44:29 +00:00
jasper
c0d71858db update MASTER_SITES where distfiles.nl was used 2020-01-26 11:14:29 +00:00
jca
df2845d7c6 Move EMBOSS programs to /usr/local/libexec/emboss/
EMBOSS ships a lot of programs with generic names, it conflicts with
devel/pscan and also the upcoming texlive update.  People who use EMBOSS
can change their PATH.  Suggested by sthen@, ok edd@ sthen@
2019-11-11 17:35:10 +00:00
cwen
9bf3f6048c p5-Bio-ASN1-EntrezGene: fix unescaped left braces in regexes that
generated warnings that made tests failing.

OK sthen@
2019-08-09 16:03:10 +00:00
sthen
9fe1e38b23 replace simple PERMIT_PACKAGE_CDROM=Yes with PERMIT_PACKAGE=Yes 2019-07-12 20:43:27 +00:00
kmos
c45cd79fc7 Add RUN_DEPENDS to TEST_DEPENDS automatically for ports using the
lang/python port module. I've not yet come up with a port that
would not need this and one can always set MODPY_TESTDEP to "no"
to prevent the module from touching TEST_DEPENDS.

Idea from afresh1 who pointed out the cpan module already does this.

aja "I support this move."

OK sthen@
2019-05-15 12:04:34 +00:00
danj
d696214158 Remove maintainer per their request 2019-05-10 16:50:05 +00:00
cwen
d00e4f9c95 bioperl: unbreak tests, fix runtime with Perl 5.28, move HOMEPAGE to https
Thanks to afresh1@ for patches and hints!

OK afresh1@
2019-02-21 10:25:48 +00:00
naddy
ea48ea6774 don't pick up gd if it happens to be installed 2018-11-29 20:15:25 +00:00
sthen
25f0e460f2 Add COMPILER lines to c++ ports which currently use the default. Adjust
some existing COMPILER lines with arch restrictions etc. In the usual
case this is now using "COMPILER = base-clang ports-gcc base-gcc" on
ports with c++ libraries in WANTLIB.

This is basically intended to be a noop on architectures using clang
as the system compiler, but help with other architectures where we
currently have many ports knocked out due to building with an unsuitable
compiler -

- some ports require c++11/newer so the GCC version in base that is used
on these archirtectures is too old.

- some ports have conflicts where an executable is built with one compiler
(e.g. gcc from base) but a library dependency is built with a different
one (e.g. gcc from ports), resulted in mixing incompatible libraries in the
same address space.

devel/gmp is intentionally skipped as it's on the path to building gcc -
the c++ library there is unused in ports (and not built by default upstream)
so intending to disable building gmpcxx in a future commit.
2018-10-24 14:27:57 +00:00
sthen
5e964ab0df bump LIBCXX/LIBECXX/COMPILER_LIBCXX ports. 2017-07-26 22:45:14 +00:00
espie
8ac47fd9c6 use COMPILER_LIBCXX where applicable 2017-07-16 19:18:47 +00:00
sthen
7b9fdbb2c9 use LIBCXX 2017-04-10 11:45:22 +00:00
jca
70908165e6 Don't hardcode g++ 2017-02-27 11:27:25 +00:00
sthen
a1ff17ec85 fix biology/hmmer packaging on !amd64 (impl_sse.h is not produced) 2016-11-25 20:42:57 +00:00
jca
065deff2a7 +hmmer 2016-11-22 11:07:10 +00:00
jca
1ca0ede4a9 Import HMMER, a Hidden Markov Model toolkit.
Port from maintainer Senthil Kumar M with tweaks from sthen@ and I.
ok sthen@

HMMER is used for searching sequence databases for sequence homologs,
and for making sequence alignments. It implements methods using
probabilistic models called profile hidden Markov models (profile
HMMs). HMMER is designed to detect remote homologs as sensitively as
possible, relying on the strength of its underlying probability
models.

HMMER is often used together with a profile database, such as Pfam
or many of the databases that participate in Interpro. But HMMER
can also work with query sequences, not just profiles, just like
BLAST. For example, you can search a protein query sequence against
a database with phmmer, or do an iterative search with jackhmmer.
2016-11-22 11:05:51 +00:00
sthen
46e13aac66 sprinkle some deps on www/p5-CGI 2016-04-05 12:21:40 +00:00
naddy
cfbb239b6a Remove SHARED_ONLY from all CPAN Perl ports and the cpan and perl MODULES.
Add WANTLIB+=perl and PKG_ARCH=* as appropriate.
2016-03-20 19:56:05 +00:00
naddy
deea7ed07b drop SHARED_ONLY from python and ruby ports 2016-03-20 16:12:22 +00:00
ajacoutot
1ef81463b6 Consistent email address. 2016-01-12 13:19:37 +00:00
jasper
a701818e72 - "update" homepage; however the new homepage doesn't contain any working
links to a release and many pages are broken
- tell portroach to ignore this port
2016-01-10 16:28:59 +00:00
ajacoutot
399fbd8868 print/py-reportlab/reportlab -> print/py-reportlab 2016-01-05 13:24:05 +00:00
ajacoutot
c0ff75b9a6 Update to biopython-1.66. 2015-11-29 08:22:11 +00:00
sthen
12fa514550 sync WANTLIB 2015-08-19 20:34:33 +00:00
jasper
c8ddb2afd7 update to biopython-1.65 2015-07-18 22:24:48 +00:00
jasper
a825ad7359 update to nutdb-20.1 2015-05-09 08:31:34 +00:00