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Sat, 3 Aug 2024 08:27:34 GMT (envelope-from git) Date: Sat, 3 Aug 2024 08:27:34 GMT Message-Id: <202408030827.4738RY6R081437@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: 086a436ba451 - main - biology/fermi-lite: New port: Library anf tool for assembling Illumina short reads in small regions 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: 086a436ba4517c1f068a99669a9aabc727ebf2df Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=086a436ba4517c1f068a99669a9aabc727ebf2df commit 086a436ba4517c1f068a99669a9aabc727ebf2df Author: Yuri Victorovich AuthorDate: 2024-08-03 05:31:51 +0000 Commit: Yuri Victorovich CommitDate: 2024-08-03 08:27:25 +0000 biology/fermi-lite: New port: Library anf tool for assembling Illumina short reads in small regions --- biology/Makefile | 1 + biology/fermi-lite/Makefile | 39 +++++++++++++++++++++++++++++++++++++++ biology/fermi-lite/distinfo | 3 +++ biology/fermi-lite/pkg-descr | 8 ++++++++ 4 files changed, 51 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 2a6da67d4b30..faa2b7ac520f 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -60,6 +60,7 @@ SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit + SUBDIR += fermi-lite SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate diff --git a/biology/fermi-lite/Makefile b/biology/fermi-lite/Makefile new file mode 100644 index 000000000000..86512a27552a --- /dev/null +++ b/biology/fermi-lite/Makefile @@ -0,0 +1,39 @@ +PORTNAME= fermi-lite +DISTVERSIONPREFIX= v +DISTVERSION= 0.1-13 +DISTVERSIONSUFFIX= -g85f159e +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Library and tool for assembling Illumina short reads in small regions +WWW= https://github.com/lh3/fermi-lite + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +USES= gmake +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +MAKE_ARGS= CFLAGS="${CFLAGS}" + +BINARY_ALIAS= gcc=${CC} + +PLIST_FILES= bin/fml-asm \ + include/fml.h \ + lib/libfml.a \ + lib/libfml.so + +post-build: + @cd ${WRKSRC} && \ + ${CC} ${CFLAGS} -fPIC ${LDFLAGS} -shared $$(ls *.c | grep -v example.c) -o libfml.so + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/fml-asm ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/fml.h ${STAGEDIR}${PREFIX}/include + ${INSTALL_DATA} ${WRKSRC}/libfml.a ${STAGEDIR}${PREFIX}/lib + ${INSTALL_LIB} ${WRKSRC}/libfml.so ${STAGEDIR}${PREFIX}/lib + +.include diff --git a/biology/fermi-lite/distinfo b/biology/fermi-lite/distinfo new file mode 100644 index 000000000000..a2bcd5b34a70 --- /dev/null +++ b/biology/fermi-lite/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1722640889 +SHA256 (lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz) = eafa2f290c3857bcae4804fa3e86c59b8437777835cc601699d78e2192ca44fd +SIZE (lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz) = 248339 diff --git a/biology/fermi-lite/pkg-descr b/biology/fermi-lite/pkg-descr new file mode 100644 index 000000000000..f020c272f73e --- /dev/null +++ b/biology/fermi-lite/pkg-descr @@ -0,0 +1,8 @@ +Fermi-lite is a standalone C library as well as a command-line tool for +assembling Illumina short reads in regions from 100bp to 10 million bp in size. +It is largely a light-weight in-memory version of fermikit without generating +any intermediate files. It inherits the performance, the relatively small memory +footprint and the features of fermikit. In particular, fermi-lite is able to +retain heterozygous events and thus can be used to assemble diploid regions for +the purpose of variant calling. It is one of the limited choices for local +re-assembly and arguably the easiest to interface.