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References: <20210606051407.6535-1-madalinionel.patrascu@mdc-berlin.de> In-Reply-To: <20210606051407.6535-1-madalinionel.patrascu@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Jun 2021 07:34:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48862 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <48862@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 48862-submit@debbugs.gnu.org id=B48862.16229648013290 (code B ref 48862); Sun, 06 Jun 2021 07:34:02 +0000 Received: (at 48862) by debbugs.gnu.org; 6 Jun 2021 07:33:21 +0000 Received: from localhost ([127.0.0.1]:50525 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpnHZ-0000qu-1v for submit@debbugs.gnu.org; Sun, 06 Jun 2021 03:33:21 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50511) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpnHT-0000qZ-R0 for 48862@debbugs.gnu.org; Sun, 06 Jun 2021 03:33:16 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 4C2CD1600BE; Sun, 6 Jun 2021 09:33:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1622964780; x=1624779181; bh=izlurZLe3nP40yIAkKO4c2SwUaOWFzTusSEnUwQySM8=; b=CoJ2uejFTeqf HjiRJaHTCPLeslzClOxzHt9Lx3Lry4tHUOvUn5pR6E8sT1LgCF8bggzE1eH2kncm zjBm/RwXjh+TOIRTrdpxsUC4VqVLbH1hQxDODfbpeuD52AUhDQu9h6eY0FkW4V8p E7rHZdYdrJh9dd5GiXguNiTds4porLM= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id TyXLMAwzuUQ4; Sun, 6 Jun 2021 09:33:00 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS; Sun, 6 Jun 2021 09:33:00 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2242.10; Sun, 6 Jun 2021 09:33:00 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 6 Jun 2021 09:32:53 +0200 Message-ID: <20210606073253.18811-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-26202.006 X-TM-AS-Result: No-10--1.293000-8.000000 X-TMASE-MatchedRID: HQtbll+gJ6+6/eEqqZaZmmvOwg12ikVSpAWTmiZjiA04rjJc1YXhsHyW 4nmnhJxPcHBBBf/rw+Z/6kMd15bGDDbcsMCH+ZLF2pDoO7oaT7NLXPA26IG0hKMQi364g884Ay7 Fge6wFltKe2x1m1lgB/0TcPpf7aMdbbH8KGCkYT6dVNZaI2n6/wH9Qt+fIXSvXplsKAlw4/UQi6 wXM/8Y9f8lqKDjhCPxxtgTkG+GaOcsiCsmh7kHt00/Wb3kjwMV4k1wcu9E2kTz5QKK9iuho+LPL vmXofmpfS0Ip2eEHnz3IzXlXlpamPoLR4+zsDTttrrTuahHzlE5eZlxG8S+Qn5jbhq3eK8JmQli 1XwCxVc9O62Z945KsM5sjjD2BxRUTroHhSVl+W7f3XVkzHNN8ydsq5FK2r09Pz74SmX+niRvx+y 4SCozttG1pfB9ENkTtDC+Oypvl/RGDgEFwm6aoD6Qrn3xh/cy X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.293000-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.006 X-TM-SNTS-SMTP: 6F0030F75190F7D54B16D7A26F26E3282868AAEC37A26BD3D53F0CF55384D95A2000:F 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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. [source]: Changed from pypi to github, pypi sources do not contain tests. [arguments]: Add build phase "patch-test-data" and removed #:tests? #f. [propagated-inputs]: Add python-h5py, python-numpy, python-pandas and python-scipy. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..66e69ff2c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C data.") (define-public python-hic2cool (package (name "python-hic2cool") - (version "0.4.2") + (version "0.8.3") + ;; pypi sources do not contain the test_data directory and no test can be + ;; run (source (origin - (method url-fetch) - (uri (pypi-uri "hic2cool" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/4dn-dcic/hic2cool") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) + "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl")))) (build-system python-build-system) - (arguments '(#:tests? #f)) ; no tests included + (arguments + `(#:phases + (modify-phases %standard-phases + ;;two of the test-data files need to be writable + (add-after 'unpack 'patch-test-data + (lambda* (#:key inputs outputs #:allow-other-keys) + (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600) + (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600)))))) (propagated-inputs - `(("python-cooler" ,python-cooler))) + `(("python-cooler" ,python-cooler) + ("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy))) (home-page "https://github.com/4dn-dcic/hic2cool") (synopsis "Converter for .hic and .cool files") (description