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Sat, 7 Sep 2024 21:31:13 GMT (envelope-from git) Date: Sat, 7 Sep 2024 21:31:13 GMT Message-Id: <202409072131.487LVDLa069084@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 7989e8dd3d93 - main - biology/andi: New ports: Efficient estimation of evolutionary distances 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: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 7989e8dd3d93eae1f8b75112032aed09c85ecd89 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=7989e8dd3d93eae1f8b75112032aed09c85ecd89 commit 7989e8dd3d93eae1f8b75112032aed09c85ecd89 Author: Yuri Victorovich AuthorDate: 2024-09-07 21:29:14 +0000 Commit: Yuri Victorovich CommitDate: 2024-09-07 21:31:10 +0000 biology/andi: New ports: Efficient estimation of evolutionary distances --- biology/Makefile | 1 + biology/andi/Makefile | 32 ++++++++++++++++++++++++++++++++ biology/andi/distinfo | 3 +++ biology/andi/pkg-descr | 4 ++++ 4 files changed, 40 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 2415e6d7a85c..0c097ae77b3b 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -5,6 +5,7 @@ SUBDIR += R-cran-BiocManager SUBDIR += abyss SUBDIR += ad2vcf + SUBDIR += andi SUBDIR += artemis SUBDIR += atac-seq SUBDIR += augustus diff --git a/biology/andi/Makefile b/biology/andi/Makefile new file mode 100644 index 000000000000..ceb195bab1ca --- /dev/null +++ b/biology/andi/Makefile @@ -0,0 +1,32 @@ +PORTNAME= andi +DISTVERSIONPREFIX= v +DISTVERSION= 0.14-3 +DISTVERSIONSUFFIX= -g390af15 +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Efficient estimation of evolutionary distances +WWW= https://github.com/EvolBioInf/andi + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libdivsufsort.so:math/libdivsufsort \ + libgsl.so:math/gsl + +USES= autoreconf gmake localbase pkgconfig +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= EvolBioInf + +GNU_CONFIGURE= yes + +OPTIONS_DEFINE= DOCS + +PORTDOCS= * + +PLIST_FILES= bin/andi \ + share/man/man1/andi.1.gz + +.include diff --git a/biology/andi/distinfo b/biology/andi/distinfo new file mode 100644 index 000000000000..461c52657f4f --- /dev/null +++ b/biology/andi/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1725743879 +SHA256 (EvolBioInf-andi-v0.14-3-g390af15_GH0.tar.gz) = 7373445abd107bbc7fed2f3f01e3dbc34955089cf0690e26beb16bd4014b39ce +SIZE (EvolBioInf-andi-v0.14-3-g390af15_GH0.tar.gz) = 539569 diff --git a/biology/andi/pkg-descr b/biology/andi/pkg-descr new file mode 100644 index 000000000000..4d20c8c9b327 --- /dev/null +++ b/biology/andi/pkg-descr @@ -0,0 +1,4 @@ +andi is a program for estimating the evolutionary distance between closely +related genomes. These distances can be used to rapidly infer phylogenies +for big sets of genomes. Because andi does not compute full alignments, +it is so efficient that it scales even up to thousands of bacterial genomes.