From owner-dev-commits-ports-all@freebsd.org Sun Apr 18 13:53:40 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id F32EF5EA625; Sun, 18 Apr 2021 13:53:40 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FNWd06YRdz3hdt; Sun, 18 Apr 2021 13:53:40 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id C91EA4CEC; Sun, 18 Apr 2021 13:53:40 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13IDrexh054778; Sun, 18 Apr 2021 13:53:40 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13IDreDb054777; Sun, 18 Apr 2021 13:53:40 GMT (envelope-from git) Date: Sun, 18 Apr 2021 13:53:40 GMT Message-Id: <202104181353.13IDreDb054777@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 49a1ada63293 - main - biology/readseq: Read and reformat biosequences, Java command-line version MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 49a1ada63293e4c27a396fb8997a238dd090e7de Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 18 Apr 2021 13:53:41 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=49a1ada63293e4c27a396fb8997a238dd090e7de commit 49a1ada63293e4c27a396fb8997a238dd090e7de Author: Jason W. Bacon AuthorDate: 2021-04-18 13:52:41 +0000 Commit: Jason W. Bacon 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 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