From owner-freebsd-ports-bugs@freebsd.org Wed Feb 10 22:40:54 2016 Return-Path: Delivered-To: freebsd-ports-bugs@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id CF387AA499A for ; Wed, 10 Feb 2016 22:40:54 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2001:1900:2254:206a::16:76]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id C1320181F for ; Wed, 10 Feb 2016 22:40:54 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from bugs.freebsd.org ([127.0.1.118]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id u1AMes8I062667 for ; Wed, 10 Feb 2016 22:40:54 GMT (envelope-from bugzilla-noreply@freebsd.org) From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 207032] [change request] biology/samtools: add samtools headers Date: Wed, 10 Feb 2016 22:40:54 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: changed X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Some People X-Bugzilla-Who: bacon4000@gmail.com X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: freebsd-ports-bugs@FreeBSD.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: Message-ID: In-Reply-To: References: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated MIME-Version: 1.0 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.20 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 10 Feb 2016 22:40:54 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D207032 --- Comment #10 from Jason Bacon --- A lot of biology software developers don't yet understand the value of pack= age managers, so a common approach is bundle all the dependencies and run the software from the build directory. Biology + computer science is a relativ= ely new relationship for the most part. Older versions of samtools did install the headers. I suspect the develope= rs just fell in line with the bundling approach and just didn't bother to add = it to the newer Makefiles. I intend to send the patches upstream so the next version will install the library and headers. A port option would not be useful. If the library and headers are not available by default, then ports that depend on them (e.g. RSEM) will have = to build and use their own bundled samtools in order to be packaged. This is = what I'm trying to avoid. Thanks, Jason --=20 You are receiving this mail because: You are the assignee for the bug.=