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Tue, 10 Dec 2024 20:33:28 GMT (envelope-from git) Date: Tue, 10 Dec 2024 20:33:28 GMT Message-Id: <202412102033.4BAKXSoo083442@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: f7b1e0ec49b6 - main - biology/hyphy: Update to 2.5.64 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: f7b1e0ec49b6360f713428b32d6aad2f514a50f8 Auto-Submitted: auto-generated The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=f7b1e0ec49b6360f713428b32d6aad2f514a50f8 commit f7b1e0ec49b6360f713428b32d6aad2f514a50f8 Author: Älven AuthorDate: 2024-11-28 17:38:16 +0000 Commit: Joseph Mingrone CommitDate: 2024-12-10 20:31:58 +0000 biology/hyphy: Update to 2.5.64 PR: 283028 --- biology/hyphy/Makefile | 5 +++-- biology/hyphy/distinfo | 6 +++--- biology/hyphy/pkg-plist | 10 ++++++---- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index f8c26082e883..b18cba727f82 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,10 +1,11 @@ PORTNAME= hyphy -DISTVERSION= 2.5.63 +DISTVERSION= 2.5.64 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org COMMENT= Hypothesis testing using Phylogenies -WWW= https://www.hyphy.org/ +WWW= https://www.hyphy.org/ \ + https://github.com/veg/hyphy/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index e765dff23918..ffa4bb48bcc2 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1729872359 -SHA256 (veg-hyphy-2.5.63_GH0.tar.gz) = 86a94a601fa136443a8cd69f61e3a47b1dc85f10743d317715b1e433278e9ee0 -SIZE (veg-hyphy-2.5.63_GH0.tar.gz) = 5607295 +TIMESTAMP = 1732814990 +SHA256 (veg-hyphy-2.5.64_GH0.tar.gz) = 7ba1aaf82c8d876d36dc9deb63da8a5da604917fe1628cef444af0207579aea6 +SIZE (veg-hyphy-2.5.64_GH0.tar.gz) = 5613927 diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist index 3491aaa1b191..2f58e0cb50d2 100644 --- a/biology/hyphy/pkg-plist +++ b/biology/hyphy/pkg-plist @@ -129,6 +129,9 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/LZ_Complexity.bf %%DATADIR%%/TemplateBatchFiles/LocalMolClock.bf %%DATADIR%%/TemplateBatchFiles/MGvsGY.bf +%%DATADIR%%/TemplateBatchFiles/MSS-joint-fitter.bf +%%DATADIR%%/TemplateBatchFiles/MSS-selector-2.bf +%%DATADIR%%/TemplateBatchFiles/MSS-selector.bf %%DATADIR%%/TemplateBatchFiles/MergeSequences.bf %%DATADIR%%/TemplateBatchFiles/MergeSites.bf %%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf @@ -147,9 +150,6 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/ModelTest.bf %%DATADIR%%/TemplateBatchFiles/MolClockAllRoots.bf %%DATADIR%%/TemplateBatchFiles/MolecularClock.bf -%%DATADIR%%/TemplateBatchFiles/MSS-joint-fitter.bf -%%DATADIR%%/TemplateBatchFiles/MSS-selector-2.bf -%%DATADIR%%/TemplateBatchFiles/MSS-selector.bf %%DATADIR%%/TemplateBatchFiles/NeighborJoining.bf %%DATADIR%%/TemplateBatchFiles/NielsenYang.bf %%DATADIR%%/TemplateBatchFiles/NucModelCompare.bf @@ -181,8 +181,8 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FADE.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FEL.bf -%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/MEME.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/PRIME.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf @@ -389,6 +389,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/libv3/models/binary/empirical.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/BS_REL.bf +%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_GTR.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf @@ -416,6 +417,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/libv3/tasks/distances.bf %%DATADIR%%/TemplateBatchFiles/libv3/tasks/estimators.bf %%DATADIR%%/TemplateBatchFiles/libv3/tasks/genetic_code.bf +%%DATADIR%%/TemplateBatchFiles/libv3/tasks/mapping.bf %%DATADIR%%/TemplateBatchFiles/libv3/tasks/mpi.bf %%DATADIR%%/TemplateBatchFiles/libv3/tasks/trees.bf %%DATADIR%%/TemplateBatchFiles/molclockBootstrap.bf