From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:51448) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igz3z-0000pL-4y for guix-patches@gnu.org; Mon, 16 Dec 2019 17:42:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igz3y-0001PH-2A for guix-patches@gnu.org; Mon, 16 Dec 2019 17:42:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34480) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1igz3x-0001NQ-Op for guix-patches@gnu.org; Mon, 16 Dec 2019 17:42:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1igz3x-0006fv-Ly for guix-patches@gnu.org; Mon, 16 Dec 2019 17:42:01 -0500 Subject: [bug#38505] [PATCH] gnu: Add fast-screen. Resent-Message-ID: References: <20191205212114.4971-1-madalinionel.patrascu@mdc-berlin.de> From: Ricardo Wurmus In-reply-to: <20191205212114.4971-1-madalinionel.patrascu@mdc-berlin.de> Date: Mon, 16 Dec 2019 23:41:47 +0100 Message-ID: <87immfc2qc.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Cc: 38505@debbugs.gnu.org Hi M=C4=83d=C4=83lin, > * gnu/packages/bioinformatics.scm (fast-screen): New variable. I don=E2=80=99t think this package actually produces a usable output. Frustratingly, this is a Perl script which calls out to tools that happen to be on the user=E2=80=99s PATH, such as Bismark (which is written = in the same style, so it may be enlightening to read its package definition), bwa, or bowtie. Simply copying the script to the store won=E2=80=99t yield a usable tool I= =E2=80=99m afraid. For Bismark I talked to the authors in the past in the hopes of simplifying configuration at build time, but they were not interested in changing the tool to accomodate any other case than the one Bismark was designed for: to be unpacked in an already suitable environment. This means that we can=E2=80=99t count on upstream to change this and patch= the source file by ourselves. One way is to patch every invocation of an external command; another is to wrap the script itself (with =E2=80=9Cwrap-script=E2=80=9D) in PATH and PERL5PATH to provide a suitable = environment at runtime. (Wrapping PERL5PATH may be necessary anyway to ensure that Perl can find the required modules.) Good luck! -- Ricardo