Date: Sun, 18 Apr 2021 13:53:40 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 49a1ada63293 - main - biology/readseq: Read and reformat biosequences, Java command-line version Message-ID: <202104181353.13IDreDb054777@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=49a1ada63293e4c27a396fb8997a238dd090e7de commit 49a1ada63293e4c27a396fb8997a238dd090e7de Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-04-18 13:52:41 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-04-18 13:53:02 +0000 biology/readseq: Read and reformat biosequences, Java command-line version Sequence reading library developed by the Ribosomal Database Project. It can handle genbank, embl, fasta, fastq, sff and sto files, can read from files or streams, and can handle indexing files. --- biology/Makefile | 1 + biology/readseq/Makefile | 26 ++++++++++++++++++++++++++ biology/readseq/distinfo | 3 +++ biology/readseq/files/readseq.in | 3 +++ biology/readseq/pkg-descr | 5 +++++ 5 files changed, 38 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index adb71952bb1e..956405f7e693 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -148,6 +148,7 @@ SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler + SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio diff --git a/biology/readseq/Makefile b/biology/readseq/Makefile new file mode 100644 index 000000000000..5956dbea4551 --- /dev/null +++ b/biology/readseq/Makefile @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= readseq +DISTVERSION= 2.1.19 +CATEGORIES= biology java +# The site used by bioconda for 2.1.30 is down as of 2021-04-13 +# MASTER_SITES= http://iubio.bio.indiana.edu/soft/molbio/readseq/java/ +MASTER_SITES= https://sourceforge.net/projects/readseq/files/latest/ +DISTNAME= ${PORTNAME} +EXTRACT_SUFX= .jar + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Read and reformat biosequences, Java command-line version + +LICENSE= PD + +USE_JAVA= yes +NO_BUILD= yes +SUB_FILES= readseq +PLIST_FILES= bin/readseq share/java/classes/readseq.jar + +do-install: + ${INSTALL_DATA} ${DISTDIR}/${DISTFILES} ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_SCRIPT} ${WRKDIR}/readseq ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/readseq/distinfo b/biology/readseq/distinfo new file mode 100644 index 000000000000..a4a40484d345 --- /dev/null +++ b/biology/readseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1618350447 +SHA256 (readseq.jar) = 966e7d4e1c4c6add588b3ead281c993c6a0c35b991a1ded53f81230a54ac6778 +SIZE (readseq.jar) = 767702 diff --git a/biology/readseq/files/readseq.in b/biology/readseq/files/readseq.in new file mode 100755 index 000000000000..41d8d2466c57 --- /dev/null +++ b/biology/readseq/files/readseq.in @@ -0,0 +1,3 @@ +#!/bin/sh -e + +java -jar %%JAVAJARDIR%%/readseq.jar "$@" diff --git a/biology/readseq/pkg-descr b/biology/readseq/pkg-descr new file mode 100644 index 000000000000..f07d55783e38 --- /dev/null +++ b/biology/readseq/pkg-descr @@ -0,0 +1,5 @@ +Sequence reading library developed by the Ribosomal Database Project. It can +handle genbank, embl, fasta, fastq, sff and sto files, can read from files or +streams, and can handle indexing files. + +WWW: https://sourceforge.net/projects/readseq
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202104181353.13IDreDb054777>