From nobody Mon Sep 13 13:43:39 2021 X-Original-To: ports-bugs@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id DF5E217A45DE for ; Mon, 13 Sep 2021 13:43:39 +0000 (UTC) (envelope-from bugzilla-noreply@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 4H7SP75tdwz3MMQ for ; Mon, 13 Sep 2021 13:43:39 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2610:1c1:1:606c::50:1d]) (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 AAB6627CF7 for ; Mon, 13 Sep 2021 13:43:39 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org ([127.0.1.5]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id 18DDhdJC049625 for ; Mon, 13 Sep 2021 13:43:39 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id 18DDhdJi049623 for ports-bugs@FreeBSD.org; Mon, 13 Sep 2021 13:43:39 GMT (envelope-from bugzilla-noreply@freebsd.org) X-Authentication-Warning: kenobi.freebsd.org: www set sender to bugzilla-noreply@freebsd.org using -f From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 258478] biology/emboss: Add wrapper to eliminate need for altered PATH Date: Mon, 13 Sep 2021 13:43:39 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new 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: jwb@freebsd.org X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: wen@FreeBSD.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter flagtypes.name attachments.created Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated List-Id: Ports bug reports List-Archive: https://lists.freebsd.org/archives/freebsd-ports-bugs List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-ports-bugs@freebsd.org X-BeenThere: freebsd-ports-bugs@freebsd.org MIME-Version: 1.0 X-ThisMailContainsUnwantedMimeParts: N https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D258478 Bug ID: 258478 Summary: biology/emboss: Add wrapper to eliminate need for altered PATH Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Some People Priority: --- Component: Individual Port(s) Assignee: wen@FreeBSD.org Reporter: jwb@freebsd.org Flags: maintainer-feedback?(wen@FreeBSD.org) Assignee: wen@FreeBSD.org Created attachment 227873 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D227873&action= =3Dedit Unified diff adding C wrapper The attached patch turns emboss commands into subcommands much like those u= sed by bwa, samtools, bedtools, etc. This allows users to run emboss commands without altering their PATH, and allows simultaneous access to conflicting commands such as /usr/local/bin/garnier and /usr/local/emboss/bin/garnier. E.g. emboss garnier # Runs /usr/local/emboss/bin/garnier garnier # Runs /usr/local/bin/garnier (from biology/fasta) --=20 You are receiving this mail because: You are the assignee for the bug.=