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Resent-From: Maxim Cournoyer Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 18 Mar 2022 04:14:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38505 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: Ricardo Wurmus Cc: 38505@debbugs.gnu.org, =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 38505-submit@debbugs.gnu.org id=B38505.164757682524424 (code B ref 38505); Fri, 18 Mar 2022 04:14:02 +0000 Received: (at 38505) by debbugs.gnu.org; 18 Mar 2022 04:13:45 +0000 Received: from localhost ([127.0.0.1]:55958 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nV3zl-0006Ls-GF for submit@debbugs.gnu.org; Fri, 18 Mar 2022 00:13:45 -0400 Received: from mail-qt1-f174.google.com ([209.85.160.174]:45728) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nV3zj-0006Le-RQ for 38505@debbugs.gnu.org; Fri, 18 Mar 2022 00:13:44 -0400 Received: by mail-qt1-f174.google.com with SMTP id a11so2150556qtb.12 for <38505@debbugs.gnu.org>; Thu, 17 Mar 2022 21:13:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version:content-transfer-encoding; bh=gueRV8YPaA9a9MurWL9KUx23zTm/rkUBOtISjnthVB4=; b=NipAaR5sPtlZTMcguRDf6mTBZeq4O//amo5lZbQxu1k3HPWlWbeKfFGrBY1vm0AHuB 32hBxi2H4MDQpqlOnbiq2PDXowEz6Xcm2oeyoH1UidpQWfS4z/BFWyr5Ku0n5abDi3nA ckRfbVkCg5C+jlcSm2tNdrLGRysgrQcHSbeJ1ji+vExIR1auHBkBC9ps6EZTJqzLisqY MZpqg/y3fIcqIszFDwCMmrVovHsU4f7+vpKF7QdJH3JY8D4RilmfUtiY8EEskkMFKH9x h+XfSLhhQ6MonNlqlQ30e3lNndb43diVteQX6AJj/RzFZQDFkj006Va8Z5GJvpxHsAyV ceNg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version:content-transfer-encoding; bh=gueRV8YPaA9a9MurWL9KUx23zTm/rkUBOtISjnthVB4=; b=WIfmUAHculsHbmc/JTkDE09iYy5vnzMimW1wAFfd+N7pAfrB0bLY1YH+OSpi1ixZMU x3fY6Om+qXalspcPAd8tdoRrT37i1moPx8BBV/m2RLcLjNCKX0bNOha20wsduWo99A0J UpFFRdp1ffRwh+yEKoYTdhyzOJCNLk6nOOB1L+ZPlo4s+ImFd1TOXOX+sEUbcqKVkzJQ nULXRVGaQ7MEtK2wEOCpwh0MyMi6r9mr3OXWGYRCh/LHRMZaZTMCCTCBJuFivx83HWtJ lCoSFiHZP6/IC4PfQIdhasGdN8SA8SxpirEcR3PlXpLwJ9wSU42A1rleR2LjcBQ6jxxH vP/w== X-Gm-Message-State: AOAM533U6RAJncfOgL777aYxkHnxBvjXKVLd0K4Mbk0yHmrpTChOx8VE IostIn5BHMP3XN3dNzrFQ+ZRFSfG3Z8JfQ== X-Google-Smtp-Source: ABdhPJwiu5qqibbnpBqdlb/WKR+xMstbv1SXseIQD47W18q/BuLzTthP43J01sW3fBmNmDqDvYOFRQ== X-Received: by 2002:ac8:5711:0:b0:2e1:cde2:6922 with SMTP id 17-20020ac85711000000b002e1cde26922mr6253919qtw.116.1647576818326; Thu, 17 Mar 2022 21:13:38 -0700 (PDT) Received: from hurd (dsl-10-131-58.b2b2c.ca. [72.10.131.58]) by smtp.gmail.com with ESMTPSA id v12-20020a05622a130c00b002e1b3ccd9adsm5251738qtk.79.2022.03.17.21.13.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 17 Mar 2022 21:13:38 -0700 (PDT) From: Maxim Cournoyer References: <20191205212114.4971-1-madalinionel.patrascu@mdc-berlin.de> <87immfc2qc.fsf@elephly.net> Date: Fri, 18 Mar 2022 00:13:37 -0400 In-Reply-To: <87immfc2qc.fsf@elephly.net> (Ricardo Wurmus's message of "Mon, 16 Dec 2019 23:41:47 +0100") Message-ID: <87o8236gpa.fsf_-_@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1647576856; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=gueRV8YPaA9a9MurWL9KUx23zTm/rkUBOtISjnthVB4=; b=p3TYD4wI6tmNoAI4mcqyQvZP7Ft2hVVQLSupVAnwrW2DPLSAQlp/80wX+9fBiCwKkE7If/ 83mPd439aLh8uAd/8MK/AujKfKyoj2lw73VfRU8096sQwNitE4nboW6Xk5VmJI8CzEddiD yzJFKYrrWrX8aqTRyY1J4/4bDMO2cj+XjI0rK4dSCmVcaGJ7ijZx3b5Xk3aadXzqhnuRus rRbegmPZl8cakGVYeckTMLAX8mifzuPIQHWTQi9FMDUII+yFHVo0KFp2ZAzQaBpCHbqvxi JtuD41fV25I2BANx8tXN0PqX5rCyhBOyUvzfEUHSvp8dMSj9fWYalRay0WS8dg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1647576856; a=rsa-sha256; cv=none; b=jRf1rYFAxvIGKU88sMmwa+IFuviI2LJ94d/R2/5K5l34leLZ74LbCOB37a33Rwv6GOwJoq +IZl7lo5IjNDyaCIygwuaEwQU7K8BFx+uU5DfJzLveDitCl4kTW8xYI/j7yK3SqnTLU93e x2K6aKY69Mmkicjw3Ge6eiFJzWkP/F3LqcLUNxP4sdG06Bk5uOwttRRX3XW1SYz86Hu1i+ gDgVMbbPvzHLMsDgwmlhceGbvkcQp9sWXm2w04Jve+S8MTqXkhhsCKa35FQpG8IxTJmayf oB1DPWYrXcHtzzc1xi+8B74wUsn97ibHsailBVYSqvVpvIlETNHLZhsgHj3fmA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=NipAaR5s; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 5.95 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=NipAaR5s; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 4D9DDDB94 X-Spam-Score: 5.95 X-Migadu-Scanner: scn1.migadu.com X-TUID: xQBB4+kZvpFf Hello, Ricardo Wurmus writes: > 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 writte= n 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 pat= ch 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 suitabl= e environment > at runtime. (Wrapping PERL5PATH may be necessary anyway to ensure that > Perl can find the required modules.) > > Good luck! Some 2 years later, are you still up to the challenge hinted at by Ricardo? :-) Thanks, Maxim