/ New distfiles found via the portscout scanner Mon, 3 Aug 2026 16:25:00 +0000 jwb@freebsd.org portscout v0.8.1, by Shaun Amott /jwb@freebsd.org.html Update found for port biology/bbmap: version 39.34 to 40.01 jwb@freebsd.org biology/bbmap/39.34/40.01 Mon, 3 Aug 2026 04:46:44 -0000 http://www.freshports.org/biology/bbmap/ https://kumisystems.dl.sourceforge.net/project/bbmap/BBMap_40.01.tar.gz bbmap 39.34 Mon, 3 Aug 2026 04:46:44 -0000 Mon, 3 Aug 2026 02:13:59 -0000 biology 40.01 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fbbmap /jwb@freebsd.org.html Update found for port biology/hisat2: version 2.2.2 to v2.2.3 jwb@freebsd.org biology/hisat2/2.2.2/v2.2.3 Sat, 1 Aug 2026 04:23:50 -0000 http://www.freshports.org/biology/hisat2/ https://api.github.com/repos/DaehwanKimLab/hisat2/tarball/v2.2.3 hisat2 2.2.2 Mon, 3 Aug 2026 06:08:53 -0000 Mon, 3 Aug 2026 02:14:12 -0000 biology v2.2.3 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fhisat2 /jwb@freebsd.org.html Update found for port biology/py-crossmap: version 0.7.3 to 0.7.4 jwb@freebsd.org biology/py-crossmap/0.7.3/0.7.4 Fri, 31 Jul 2026 03:52:22 -0000 http://www.freshports.org/biology/py-crossmap/ https://pypi.org/packages/source/c/crossmap/crossmap-0.7.4.tar.gz py-crossmap 0.7.3 Mon, 3 Aug 2026 05:15:35 -0000 Mon, 3 Aug 2026 02:14:11 -0000 biology 0.7.4 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fpy-crossmap /jwb@freebsd.org.html Update found for port biology/salmon: version 1.10.3 to v2.4.1 jwb@freebsd.org biology/salmon/1.10.3/v2.4.1 Thu, 30 Jul 2026 04:37:44 -0000 biology v2.4.1 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fsalmon 1.10.3 Mon, 3 Aug 2026 06:11:29 -0000 Mon, 3 Aug 2026 02:13:59 -0000 http://www.freshports.org/biology/salmon/ https://api.github.com/repos/COMBINE-lab/salmon/tarball/v2.4.1 salmon /jwb@freebsd.org.html Update found for port devel/mongo-cxx-driver: version 4.0.0 to r4.4.1 jwb@freebsd.org devel/mongo-cxx-driver/4.0.0/r4.4.1 Fri, 24 Jul 2026 04:05:03 -0000 devel r4.4.1 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=devel%2Fmongo-cxx-driver 4.0.0 Mon, 3 Aug 2026 06:11:39 -0000 Mon, 3 Aug 2026 02:32:36 -0000 http://www.freshports.org/devel/mongo-cxx-driver/ https://api.github.com/repos/mongodb/mongo-cxx-driver/tarball/r4.4.1 mongo-cxx-driver /jwb@freebsd.org.html Update found for port science/csvtk: version 0.37.0 to v0.47.0 jwb@freebsd.org science/csvtk/0.37.0/v0.47.0 Thu, 9 Jul 2026 03:14:28 -0000 science http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=science%2Fcsvtk v0.47.0 0.37.0 Mon, 3 Aug 2026 03:59:57 -0000 Mon, 3 Aug 2026 05:25:55 -0000 http://www.freshports.org/science/csvtk/ csvtk https://api.github.com/repos/golang/sys/tarball/refs/tags/v0.47.0 /jwb@freebsd.org.html Update found for port biology/ucsc-userapps: version 474 to 500 jwb@freebsd.org biology/ucsc-userapps/474/500 Wed, 8 Jul 2026 03:23:09 -0000 https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v500.src.tgz ucsc-userapps http://www.freshports.org/biology/ucsc-userapps/ Mon, 3 Aug 2026 05:02:10 -0000 Mon, 3 Aug 2026 02:14:01 -0000 474 500 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fucsc-userapps biology /jwb@freebsd.org.html Update found for port biology/bio-mocha: version 1.20 to 1.23.1 jwb@freebsd.org biology/bio-mocha/1.20/1.23.1 Sun, 5 Jul 2026 03:25:39 -0000 Mon, 3 Aug 2026 02:14:04 -0000 Mon, 3 Aug 2026 05:26:41 -0000 1.20 bio-mocha https://api.github.com/repos/samtools/bcftools/tarball/1.23.1 http://www.freshports.org/biology/bio-mocha/ http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fbio-mocha 1.23.1 biology /jwb@freebsd.org.html Update found for port biology/mmseqs2: version 17-b804f to vnatbiotech jwb@freebsd.org biology/mmseqs2/17-b804f/vnatbiotech Sat, 20 Jun 2026 19:25:28 -0000 biology vnatbiotech http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fmmseqs2 17-b804f Mon, 3 Aug 2026 05:49:24 -0000 Mon, 3 Aug 2026 02:14:06 -0000 http://www.freshports.org/biology/mmseqs2/ https://api.github.com/repos/soedinglab/MMseqs2/tarball/vNatBiotech mmseqs2 /jwb@freebsd.org.html Update found for port biology/bifrost: version 1.3.5 to paper jwb@freebsd.org biology/bifrost/1.3.5/paper Sat, 20 Jun 2026 19:19:28 -0000 biology http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fbifrost paper http://www.freshports.org/biology/bifrost/ bifrost https://api.github.com/repos/pmelsted/bifrost/tarball/paper 1.3.5 Mon, 3 Aug 2026 02:14:15 -0000 Mon, 3 Aug 2026 05:04:37 -0000 /jwb@freebsd.org.html Update found for port biology/freebayes: version 1.3.9 to v1.3.10 jwb@freebsd.org biology/freebayes/1.3.9/v1.3.10 Sat, 20 Jun 2026 19:10:46 -0000 1.3.9 Mon, 3 Aug 2026 05:09:13 -0000 Mon, 3 Aug 2026 02:14:10 -0000 http://www.freshports.org/biology/freebayes/ https://api.github.com/repos/freebayes/freebayes/tarball/v1.3.10 freebayes biology v1.3.10 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Ffreebayes /jwb@freebsd.org.html Update found for port biology/ddocent: version 2.7.8 to v2.9.8 jwb@freebsd.org biology/ddocent/2.7.8/v2.9.8 Sat, 20 Jun 2026 19:09:34 -0000 ddocent https://api.github.com/repos/jpuritz/dDocent/tarball/v2.9.8 http://www.freshports.org/biology/ddocent/ Mon, 3 Aug 2026 02:14:11 -0000 Mon, 3 Aug 2026 05:09:52 -0000 2.7.8 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fddocent v2.9.8 biology /jwb@freebsd.org.html Update found for port biology/bfc: version g20150417 to submitted-v1 jwb@freebsd.org biology/bfc/g20150417/submitted-v1 Sat, 20 Jun 2026 18:46:14 -0000 biology http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fbfc submitted-v1 g20150417 Mon, 3 Aug 2026 02:13:59 -0000 Mon, 3 Aug 2026 06:11:36 -0000 http://www.freshports.org/biology/bfc/ bfc https://api.github.com/repos/lh3/bfc/tarball/refs/tags/submitted-v1 /jwb@freebsd.org.html Update found for port biology/vcflib: version 1.0.13 to v1.0.15 jwb@freebsd.org biology/vcflib/1.0.13/v1.0.15 Sat, 20 Jun 2026 18:45:48 -0000 Mon, 3 Aug 2026 05:16:47 -0000 Mon, 3 Aug 2026 02:14:14 -0000 1.0.13 https://api.github.com/repos/vcflib/vcflib/tarball/v1.0.15 vcflib http://www.freshports.org/biology/vcflib/ v1.0.15 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fvcflib biology /jwb@freebsd.org.html Update found for port sysutils/spcm: version 0.5.8 to 0.5.9 jwb@freebsd.org sysutils/spcm/0.5.8/0.5.9 Sat, 20 Jun 2026 18:42:16 -0000 0.5.9 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=sysutils%2Fspcm sysutils https://api.github.com/repos/outpaddling/SPCM/tarball/0.5.9 spcm http://www.freshports.org/sysutils/spcm/ Mon, 3 Aug 2026 05:30:29 -0000 Mon, 3 Aug 2026 04:12:15 -0000 0.5.8 /jwb@freebsd.org.html Update found for port biology/sra-tools: version 3.4.1 to vdb-4760-2.9.7 jwb@freebsd.org biology/sra-tools/3.4.1/vdb-4760-2.9.7 Sat, 20 Jun 2026 18:12:59 -0000 3.4.1 Mon, 3 Aug 2026 02:14:15 -0000 Mon, 3 Aug 2026 05:47:20 -0000 http://www.freshports.org/biology/sra-tools/ sra-tools https://api.github.com/repos/ncbi/sra-tools/tarball/refs/tags/VDB-4760-2.9.7 biology http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fsra-tools vdb-4760-2.9.7 /jwb@freebsd.org.html Update found for port net/py-google-cloud-pubsub: version 2.32.0 to 2.39.0 jwb@freebsd.org net/py-google-cloud-pubsub/2.32.0/2.39.0 Thu, 4 Jun 2026 03:47:44 -0000 http://www.freshports.org/net/py-google-cloud-pubsub/ py-google-cloud-pubsub https://pypi.org/packages/source/g/google_cloud_pubsub/google_cloud_pubsub-2.39.0.tar.gz 2.32.0 Mon, 3 Aug 2026 03:54:03 -0000 Mon, 3 Aug 2026 05:05:03 -0000 net http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=net%2Fpy-google-cloud-pubsub 2.39.0 /jwb@freebsd.org.html Update found for port devel/py-rich-click: version 1.9.7 to 1.9.8 jwb@freebsd.org devel/py-rich-click/1.9.7/1.9.8 Fri, 29 May 2026 04:04:42 -0000 http://www.freshports.org/devel/py-rich-click/ py-rich-click https://pypi.org/packages/source/r/rich_click/rich_click-1.9.8.tar.gz 1.9.7 Mon, 3 Aug 2026 03:05:21 -0000 Mon, 3 Aug 2026 06:06:56 -0000 devel http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=devel%2Fpy-rich-click 1.9.8 /jwb@freebsd.org.html Update found for port devel/R-cran-getopt: version 1.20.4 to 1.21.1 jwb@freebsd.org devel/R-cran-getopt/1.20.4/1.21.1 Tue, 28 Apr 2026 03:17:18 -0000 Mon, 3 Aug 2026 03:01:08 -0000 Mon, 3 Aug 2026 05:28:44 -0000 1.20.4 R-cran-getopt https://stat.ethz.ch/CRAN/src/contrib/getopt_1.21.1.tar.gz http://www.freshports.org/devel/R-cran-getopt/ http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=devel%2FR-cran-getopt 1.21.1 devel /jwb@freebsd.org.html Update found for port comms/cutecom: version 0.60.0 to 1.00.0 jwb@freebsd.org comms/cutecom/0.60.0/1.00.0 Thu, 23 Apr 2026 03:47:40 -0000 Mon, 3 Aug 2026 02:15:05 -0000 Mon, 3 Aug 2026 04:54:47 -0000 0.60.0 cutecom https://gitlab.com/cutecom/cutecom/-/archive/v0.60.0-RC1/cutecom-v1.00.0-RC1.tar.bz2 http://www.freshports.org/comms/cutecom/ http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=comms%2Fcutecom 1.00.0 comms /jwb@freebsd.org.html Update found for port biology/py-pydeseq2: version 0.5.2 to 0.5.4 jwb@freebsd.org biology/py-pydeseq2/0.5.2/0.5.4 Sat, 24 Jan 2026 03:11:05 -0000 0.5.2 Mon, 3 Aug 2026 05:03:27 -0000 Mon, 3 Aug 2026 02:14:13 -0000 http://www.freshports.org/biology/py-pydeseq2/ https://pypi.org/packages/source/p/pydeseq2/pydeseq2-0.5.4.tar.gz py-pydeseq2 biology 0.5.4 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fpy-pydeseq2 /jwb@freebsd.org.html Update found for port biology/py-pywgsim: version 0.5.2 to 0.6.0 jwb@freebsd.org biology/py-pywgsim/0.5.2/0.6.0 Fri, 13 Jun 2025 03:19:23 -0000 0.6.0 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fpy-pywgsim biology Mon, 3 Aug 2026 05:03:19 -0000 Mon, 3 Aug 2026 02:14:01 -0000 0.5.2 https://pypi.org/packages/source/p/pywgsim/pywgsim-0.6.0.tar.gz py-pywgsim http://www.freshports.org/biology/py-pywgsim/ /jwb@freebsd.org.html Update found for port biology/py-dna-features-viewer: version 3.1.3 to 3.1.5 jwb@freebsd.org biology/py-dna-features-viewer/3.1.3/3.1.5 Sat, 10 May 2025 03:00:27 -0000 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fpy-dna-features-viewer 3.1.5 biology py-dna-features-viewer https://pypi.org/packages/source/d/dna_features_viewer/dna_features_viewer-3.1.5.tar.gz http://www.freshports.org/biology/py-dna-features-viewer/ Mon, 3 Aug 2026 02:14:02 -0000 Mon, 3 Aug 2026 05:28:30 -0000 3.1.3 /jwb@freebsd.org.html Update found for port biology/subread: version 2.1.0 to 2.1.1 jwb@freebsd.org biology/subread/2.1.0/2.1.1 Fri, 18 Apr 2025 03:15:15 -0000 2.1.1 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fsubread biology Mon, 3 Aug 2026 05:04:40 -0000 Mon, 3 Aug 2026 02:13:59 -0000 2.1.0 https://versaweb.dl.sourceforge.net/project/subread/subread-2.1.1/subread-2.1.1-source.tar.gz subread http://www.freshports.org/biology/subread/ /jwb@freebsd.org.html Update found for port biology/stacks: version 2.68 to 2.69 jwb@freebsd.org biology/stacks/2.68/2.69 Sat, 18 Jan 2025 03:42:59 -0000 2.68 Mon, 3 Aug 2026 02:14:18 -0000 Mon, 3 Aug 2026 05:43:33 -0000 http://www.freshports.org/biology/stacks/ stacks https://catchenlab.life.illinois.edu/stacks/source/stacks-2.69.tar.gz biology http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=biology%2Fstacks 2.69 /jwb@freebsd.org.html Update found for port devel/lnphost: version 1.0a to 1.0 jwb@freebsd.org devel/lnphost/1.0a/1.0 Mon, 4 Aug 2014 09:24:33 -0000 http://www.freebsd.org/cgi/query-pr-summary.cgi?category=ports&text=devel%2Flnphost 1.0 devel lnphost http://kaz.dl.sourceforge.net/project/lnphost/OldFiles/lnphost-1.0.zip http://www.freshports.org/devel/lnphost/ Mon, 3 Aug 2026 02:40:53 -0000 Mon, 3 Aug 2026 05:22:46 -0000 1.0a