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Jason W. Bacon
018d7f39c9 biology/pooler: Optimise DNA sequencing primer-set combinations 
Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.

Primer Pooler can:

* Check through each proposed pool for combinations that are likely to form
  dimers

* Automatically move prospective amplicons between proposed pools to reduce
  dimer formation

* Automatically search the genome sequence to find which amplicons overlap, and
  place their corresponding primers in separate pools

* Optionally keep pool sizes within a specified range

* Handle thousands of primers without being slow (useful for high-throughput
  sequencing applications)

* Do all of the above with degenerate primers too.

WWW: http://ssb22.user.srcf.net/pooler/

PR:             ports/251065
Submitted by:   Silas S. Brown <silas-freebsd@flatline.org.uk>
 2020-11-15 18:50:17 +00:00
Yuri Victorovich
bf689b58be shells/starship: Update 0.44.0 -> 0.47.0 2020-11-15 18:45:34 +00:00
Rene Ladan
a1d58205a0 Remove expired ports: 
2020-11-15 archivers/py-pyliblzma: Uses deprecated version of python
2020-11-15 databases/postgis23: Upstream no longer maintained
2020-11-15 databases/py-htsql: Uses deprecated version of python
2020-11-15 devel/bzr-fastimport: Uses deprecated version of python
2020-11-15 devel/py-ToscaWidgets: Uses deprecated version of python
2020-11-15 devel/py-calendar: Uses deprecated version of python
2020-11-15 devel/py-distorm: Uses deprecated version of python
2020-11-15 devel/py-fabric1: Uses deprecated version of python
2020-11-15 devel/py-rcsparse: Uses deprecated version of python
2020-11-15 devel/pyrex: Uses deprecated version of python
2020-11-15 japanese/py-tegaki: Uses deprecated version of python
2020-11-15 math/py-networkx1: Obsolete, please use math/py-networkx instead
2020-11-15 misc/py-progressbar231: Uses deprecated version of python
2020-11-15 multimedia/py-kaa-imlib2: Uses deprecated version of python
2020-11-15 multimedia/py-kaa-metadata: Uses deprecated version of python
2020-11-15 net-im/libtelepathy: Uses deprecated version of python
2020-11-15 security/py-mcrypt: Uses deprecated version of python
2020-11-15 www/py-beautifulsoup32: Uses deprecated version of python
2020-11-15 www/py-evernote: Uses deprecated version of python
2020-04-01 www/py-meld3: EOLed upstream
2020-11-15 www/py-requestbuilder: Uses deprecated version of python
2020-11-15 x11-toolkits/py-SquareMap: Uses deprecated version of python
 2020-11-15 18:37:28 +00:00
Yuri Victorovich
4a9b50d958 audio/gsequencer: Update 3.5.16 -> 3.6.14 2020-11-15 18:29:09 +00:00
Sunpoet Po-Chuan Hsieh
5c06b95be9 Update to 7.1.2 
- Add FULL_CACHE_DRAGONBOX option

Changes:	https://github.com/fmtlib/fmt/releases
PR:		250959
Submitted by:	Daniel Engberg <daniel.engberg.lists@pyret.net>
 2020-11-15 18:16:45 +00:00
Sunpoet Po-Chuan Hsieh
3bdcf5d9a2 Update to 1.4.2 
Changes:	https://github.com/rubjo/victor-mono/releases
PR:		251069
Submitted by:	Lewis Cook <vulcan@wired.sh> (maintainer)
 2020-11-15 18:13:41 +00:00
Sunpoet Po-Chuan Hsieh
d277953aac Fix build on aarch64 
PR:		251057
Submitted by:	mikael
 2020-11-15 18:13:37 +00:00
Sunpoet Po-Chuan Hsieh
0ac856dff9 Update to 0.1.8 
Changes:	https://github.com/ruby/reline/commits/master
PR:		250974
Submitted by:	Yasuhiro KIMURA <yasu@utahime.org> (maintainer)
 2020-11-15 18:13:32 +00:00
Sunpoet Po-Chuan Hsieh
a6e0620d4d Change RUN_DEPENDS from rubygem-rouge to rubygem-rouge324 
- Bump PORTREVISION for dependency change
 2020-11-15 18:13:28 +00:00
Sunpoet Po-Chuan Hsieh
ed1208a1ad Update to 1.2.3 
Changes:	https://github.com/WinRb/winrm-elevated/blob/master/changelog.md
 2020-11-15 18:13:23 +00:00
Sunpoet Po-Chuan Hsieh
70cface5d5 Update to 3.9.5 
Changes:	https://github.com/bblimke/webmock/blob/master/CHANGELOG.md
 2020-11-15 18:13:19 +00:00
Sunpoet Po-Chuan Hsieh
c76fb51397 Update to 3.2.0 
Changes:	https://github.com/heroku/platform-api/blob/master/CHANGELOG.md
 2020-11-15 18:13:14 +00:00
Sunpoet Po-Chuan Hsieh
187d376d92 Update to 3.25.0 
Changes:	https://github.com/rouge-ruby/rouge/releases
		https://github.com/rouge-ruby/rouge/blob/master/CHANGELOG.md
 2020-11-15 18:13:10 +00:00
Sunpoet Po-Chuan Hsieh
f0d8009875 Update to 10.0.2.0 
Changes:	https://github.com/ai/autoprefixer-rails/blob/master/CHANGELOG.md
 2020-11-15 18:13:05 +00:00
Sunpoet Po-Chuan Hsieh
fc56cf7f87 Update to 1.20.0 
Changes:	https://github.com/grosser/parallel/commits/master
 2020-11-15 18:13:01 +00:00
Sunpoet Po-Chuan Hsieh
1bc73aafeb Update to 0.2.11 
Changes:	https://github.com/inspec/train-winrm/blob/master/CHANGELOG.md
 2020-11-15 18:12:56 +00:00
Sunpoet Po-Chuan Hsieh
f03b6d931c Update to 3.3.27 
Changes:	https://github.com/inspec/train/blob/master/CHANGELOG.md
 2020-11-15 18:12:51 +00:00
Sunpoet Po-Chuan Hsieh
f0c0e1266a Update to 3.3.27 
Changes:	https://github.com/inspec/train/blob/master/CHANGELOG.md
 2020-11-15 18:12:47 +00:00
Sunpoet Po-Chuan Hsieh
f7c5e74ba2 Update to 2.2.0 
Changes:	https://github.com/googleapis/google-cloud-ruby/releases
		https://github.com/googleapis/google-cloud-ruby/blob/master/google-cloud-bigtable/CHANGELOG.md
 2020-11-15 18:12:42 +00:00
Sunpoet Po-Chuan Hsieh
1a8c809499 Update to 2.2.0 
Changes:	https://github.com/googleapis/google-cloud-ruby/releases
		https://github.com/googleapis/google-cloud-ruby/blob/master/google-cloud-pubsub/CHANGELOG.md
 2020-11-15 18:12:38 +00:00
Sunpoet Po-Chuan Hsieh
c9b367ed5b Update to 3.2020.1104 
Changes:	https://github.com/mime-types/mime-types-data/blob/master/History.md
 2020-11-15 18:12:33 +00:00
Sunpoet Po-Chuan Hsieh
bf7fe98202 Update to 3.10.16 
Changes:	https://github.com/ohler55/oj/blob/develop/CHANGELOG.md
 2020-11-15 18:12:28 +00:00
Sunpoet Po-Chuan Hsieh
25085ae289 Update to 3.12.5 
Changes:	https://github.com/chef/mixlib-install/blob/master/CHANGELOG.md
 2020-11-15 18:12:24 +00:00
Sunpoet Po-Chuan Hsieh
ba6195eca6 Update to 3.3.0 
Changes:	https://github.com/guard/listen/releases
 2020-11-15 18:12:19 +00:00
Sunpoet Po-Chuan Hsieh
c5e346969e Update to 0.49.0 
Changes:	https://github.com/googleapis/google-api-ruby-client/blob/master/CHANGELOG.md
 2020-11-15 18:12:14 +00:00
Sunpoet Po-Chuan Hsieh
ca2fc63229 Update to 0.78.0 
Changes:	https://github.com/excon/excon/blob/master/changelog.txt
 2020-11-15 18:12:09 +00:00
Sunpoet Po-Chuan Hsieh
1b0e08de50 Update to 3.2.0 
Changes:	https://github.com/ticky/ruby-emoji-regex/releases
 2020-11-15 18:12:04 +00:00
Sunpoet Po-Chuan Hsieh
c7e7853f6c Update to 13.2.0 
Changes:	https://github.com/cucumber/cucumber/blob/master/messages/CHANGELOG.md
 2020-11-15 18:12:00 +00:00
Sunpoet Po-Chuan Hsieh
df5e394785 Update to 1.5.1 
Changes:	https://github.com/Shopify/bootsnap/blob/master/CHANGELOG.md
 2020-11-15 18:11:55 +00:00
Sunpoet Po-Chuan Hsieh
0d6a0e66da Update to 2.11.606 
Changes:	https://github.com/aws/aws-sdk-ruby/releases
 2020-11-15 18:11:50 +00:00
Sunpoet Po-Chuan Hsieh
e785542dd0 Update to 1.22.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-textract/CHANGELOG.md
 2020-11-15 18:11:45 +00:00
Sunpoet Po-Chuan Hsieh
4fbf94fb0d Update to 1.52.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-storagegateway/CHANGELOG.md
 2020-11-15 18:11:41 +00:00
Sunpoet Po-Chuan Hsieh
390af6fa10 Update to 1.35.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-states/CHANGELOG.md
 2020-11-15 18:11:36 +00:00
Sunpoet Po-Chuan Hsieh
6e89246165 Update to 1.97.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-ssm/CHANGELOG.md
 2020-11-15 18:11:31 +00:00
Sunpoet Po-Chuan Hsieh
36e06d8450 Update to 1.54.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-servicecatalog/CHANGELOG.md
 2020-11-15 18:11:26 +00:00
Sunpoet Po-Chuan Hsieh
e7f0013079 Update to 1.84.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-s3/CHANGELOG.md
 2020-11-15 18:11:21 +00:00
Sunpoet Po-Chuan Hsieh
934d74eb3a Update to 1.31.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-robomaker/CHANGELOG.md
 2020-11-15 18:11:16 +00:00
Sunpoet Po-Chuan Hsieh
9dabbe983d Update to 2.11.606 
Changes:	https://github.com/aws/aws-sdk-ruby/releases
 2020-11-15 18:11:12 +00:00
Sunpoet Po-Chuan Hsieh
71c83d8cd1 Update to 3.85.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-resources/CHANGELOG.md
 2020-11-15 18:11:07 +00:00
Sunpoet Po-Chuan Hsieh
67d171e007 Update to 1.35.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-quicksight/CHANGELOG.md
 2020-11-15 18:11:02 +00:00
Sunpoet Po-Chuan Hsieh
be4fab4b5a Update to 1.38.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-polly/CHANGELOG.md
 2020-11-15 18:10:57 +00:00
Sunpoet Po-Chuan Hsieh
52e8e708cb Update to 1.19.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-personalizeruntime/CHANGELOG.md
 2020-11-15 18:10:52 +00:00
Sunpoet Po-Chuan Hsieh
e5c4669c38 Update to 1.59.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-mediaconvert/CHANGELOG.md
 2020-11-15 18:10:48 +00:00
Sunpoet Po-Chuan Hsieh
bcbadb7d9d Update to 1.16.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-managedblockchain/CHANGELOG.md
 2020-11-15 18:10:43 +00:00
Sunpoet Po-Chuan Hsieh
3827b6608c Update to 1.16.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-macie2/CHANGELOG.md
 2020-11-15 18:10:38 +00:00
Sunpoet Po-Chuan Hsieh
226ab1c60b Update to 1.40.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-lightsail/CHANGELOG.md
 2020-11-15 18:10:33 +00:00
Sunpoet Po-Chuan Hsieh
cbe94bb91e Update to 1.40.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-lexmodelbuildingservice/CHANGELOG.md
 2020-11-15 18:09:13 +00:00
Sunpoet Po-Chuan Hsieh
1634dfb35c Update to 1.18.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-kendra/CHANGELOG.md
 2020-11-15 18:09:08 +00:00
Sunpoet Po-Chuan Hsieh
5cec817f38 Update to 1.35.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-iotanalytics/CHANGELOG.md
 2020-11-15 18:09:03 +00:00
Sunpoet Po-Chuan Hsieh
a51b6795a8 Update to 1.62.0 
Changes:	https://github.com/aws/aws-sdk-ruby/blob/master/gems/aws-sdk-iot/CHANGELOG.md
 2020-11-15 18:08:59 +00:00