From unknown Sat Jun 21 05:09:00 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#64992] [PATCH] gnu: Add python-baltica. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 01 Aug 2023 13:48:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 64992 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64992@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169089764819019 (code B ref -1); Tue, 01 Aug 2023 13:48:02 +0000 Received: (at submit) by debbugs.gnu.org; 1 Aug 2023 13:47:28 +0000 Received: from localhost ([127.0.0.1]:47419 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qQpih-0004wh-MV for submit@debbugs.gnu.org; Tue, 01 Aug 2023 09:47:27 -0400 Received: from lists.gnu.org ([2001:470:142::17]:46786) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qQpif-0004wU-PI for submit@debbugs.gnu.org; Tue, 01 Aug 2023 09:47:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qQpiY-0004Du-R4 for guix-patches@gnu.org; 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Tue, 1 Aug 2023 15:46:40 +0200 From: Navid Afkhami Date: Tue, 1 Aug 2023 13:46:37 +0000 Message-ID: <4cf18f120f7829851d9bc97ce7210b04fde22f72.1690897596.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27786.006 X-TM-AS-Result: No-10--4.611500-5.000000 X-TMASE-MatchedRID: cSoPLjBYd516fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIpb wG9fIuIT4LgSdO8exMk+T46mdEugcSq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIOZYcdJgScjxKWF xEPEOC9srXnXvyie1S7gPOTbvZ4g8LTVVeVyNwJSRgPzABkqxIANTuIWZ3z/FQnWEwILrelipuz 6cn+0Ukei+i4eEYpePXK8QXOw6RzrWlVyQseCTQqubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIa8DFFIBzQ4Q2UWQMbulGSX5DcYZ9uvQQWRr7kqH6lMvIZbRacZw0O71Y3t0Sp7d0BIIz1 Cn1EpM1eVRBDPUQOVwFmflLXqSyuO5cphY4IDxgwNPlEBnFX8dfsYX7riG7IuOY0q66+BqahgjV 6si4Sxb6DZFmPYUrLrQKe71GYum8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.611500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27786.006 X-TM-SNTS-SMTP: 235EA26724B554BF5CB18D902CAB785F51C37A7C5110D286CE5BD430BA2EB2D62000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (python-baltica): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6080c899af..6d745262b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5056,6 +5056,49 @@ (define-public edirect-go-programs go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-baltica + (package + (name "python-baltica") + (version "1.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dieterich-lab/Baltica") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) + (build-system pyproject-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda _ + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively ".tests" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest" "-v" "--doctest-modules"))))))) + (propagated-inputs (list python-anndata + python-click + python-flask + python-flask-wtf + gunicorn + python-h5py + python-pysam + python-numpy + python-psutil + python-pyyaml + python-scipy + snakemake-7)) + (native-inputs (list python-pytest python-pyfakefs python-cython)) + (home-page "https://github.com/dieterich-lab/Baltica") + (synopsis "Integrated splice junction usage analysis") + (description + "This framework facilitates the execution of differential junction usage methods. +Additionally, it enables the integration of results from multiple DJU methods.") + (license license:expat))) + (define-public python-bamnostic (package (name "python-bamnostic") base-commit: 34b56974dfe720e5e30f04409ac216747d7e3f5c -- 2.34.1 From unknown Sat Jun 21 05:09:00 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Navid Afkhami Subject: bug#64992: closed ([PATCH] gnu: Add python-baltica.) Message-ID: References: <87a5va7xcu.fsf@elephly.net> <4cf18f120f7829851d9bc97ce7210b04fde22f72.1690897596.git.navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 64992 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 64992@debbugs.gnu.org Date: Wed, 02 Aug 2023 06:50:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1690959001-3000-1" This is a multi-part message in MIME format... ------------=_1690959001-3000-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #64992: [PATCH] gnu: Add python-baltica. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 64992@debbugs.gnu.org. --=20 64992: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D64992 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1690959001-3000-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 64992-done) by debbugs.gnu.org; 2 Aug 2023 06:49:17 +0000 Received: from localhost ([127.0.0.1]:48737 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qR5fY-0000lL-QA for submit@debbugs.gnu.org; Wed, 02 Aug 2023 02:49:17 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21734) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qR5fV-0000l6-6z for 64992-done@debbugs.gnu.org; Wed, 02 Aug 2023 02:49:15 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1690958949; cv=none; d=zohomail.com; s=zohoarc; b=XeA0z1pBm4w4bWPu375USM5S4wIcNab465DuLNS4k0YYylEwTbHMZSXmPEqjU6uShBf2OIH3PywOegzLbSjhGswBQtbE3Iz5ycbLjhrFk3xGHlnV6sgHp9Qfip+H916PeMbgVpwpO9uhRMmDBTrGo924rvh4e+nbrDIhcjl2JMo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1690958949; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=H8q2kfLXiZK5cYq+NmChjF+BTvl/K8VsLCNomkYMd7M=; b=VxTtbonzoc8QX3hHnE7fcCYEZJ/WHf9PmAD70IpYruTfv0sKJBbx+1bl90M8tfZdzuAyz5jae494mU8Y7Q8IDzlnusT7gknYupd40rFNcrkEI36h9L3KUJ48W27q7Eiqg0pW+6A5qGk/EWv+5/a18InyRV4GGVlMks38NP4BaUg= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1690958949; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=H8q2kfLXiZK5cYq+NmChjF+BTvl/K8VsLCNomkYMd7M=; b=JUHqra+PC8Pmmb1Axo+mpMq0xeDd+MszWbZNYqFk2Sgkxdr10+tLVCX8LFZSedeq SuNc3BfCCZDO0NeGFAYLx+xzlfYLQvSpMO3GdCUfBqn+KBk2+cHCgKeKFuY2RJTXYrU FyzIqQy4A03AAaDUh9VvjpuOcd5VAaZJz9FLtSDM= Received: from localhost (193-109-142-46.pool.kielnet.net [46.142.109.193]) by mx.zohomail.com with SMTPS id 169095894846533.91340037080067; Tue, 1 Aug 2023 23:49:08 -0700 (PDT) User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: 64992-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-baltica. Date: Wed, 02 Aug 2023 08:48:37 +0200 Message-ID: <87a5va7xcu.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 64992-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Pushed with commit 5a293d0830aa9369e388d37fe767d5bf98af01b7. Thanks for the patch! -- Ricardo ------------=_1690959001-3000-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 1 Aug 2023 13:47:28 +0000 Received: from localhost ([127.0.0.1]:47419 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qQpih-0004wh-MV for submit@debbugs.gnu.org; Tue, 01 Aug 2023 09:47:27 -0400 Received: from lists.gnu.org ([2001:470:142::17]:46786) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qQpif-0004wU-PI for submit@debbugs.gnu.org; Tue, 01 Aug 2023 09:47:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qQpiY-0004Du-R4 for guix-patches@gnu.org; Tue, 01 Aug 2023 09:47:19 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qQpiW-0000sx-LD for guix-patches@gnu.org; Tue, 01 Aug 2023 09:47:18 -0400 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; s=mdc; t=1690897621; x=1692712022; bh=vT1863UojgiZBLi ZniL4y9TWeW+gT84XQm+YszJcGfM=; b=jvBuppJvWOcvUhX7et6xz4eLzRybT8Y /IWcxzc5bVg4Y3+xts4Q9SBPcLcAMQxBLxJoIKMVlW/kd1vDCQmy1Npj3R3/rHj9 CAuCj+qOJUmTpV4PHnaO9cvbyJlcBda4tmrNEolPdW9xHc/RZUoZQ8NZ4+JICkfX 4//MAoY8g/Bs= 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 id 4A52416025F for ; Tue, 1 Aug 2023 15:47:01 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.27; Tue, 1 Aug 2023 15:46:40 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add python-baltica. Date: Tue, 1 Aug 2023 13:46:37 +0000 Message-ID: <4cf18f120f7829851d9bc97ce7210b04fde22f72.1690897596.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27786.006 X-TM-AS-Result: No-10--4.611500-5.000000 X-TMASE-MatchedRID: cSoPLjBYd516fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIpb wG9fIuIT4LgSdO8exMk+T46mdEugcSq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIOZYcdJgScjxKWF xEPEOC9srXnXvyie1S7gPOTbvZ4g8LTVVeVyNwJSRgPzABkqxIANTuIWZ3z/FQnWEwILrelipuz 6cn+0Ukei+i4eEYpePXK8QXOw6RzrWlVyQseCTQqubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIa8DFFIBzQ4Q2UWQMbulGSX5DcYZ9uvQQWRr7kqH6lMvIZbRacZw0O71Y3t0Sp7d0BIIz1 Cn1EpM1eVRBDPUQOVwFmflLXqSyuO5cphY4IDxgwNPlEBnFX8dfsYX7riG7IuOY0q66+BqahgjV 6si4Sxb6DZFmPYUrLrQKe71GYum8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.611500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27786.006 X-TM-SNTS-SMTP: 235EA26724B554BF5CB18D902CAB785F51C37A7C5110D286CE5BD430BA2EB2D62000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (python-baltica): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6080c899af..6d745262b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5056,6 +5056,49 @@ (define-public edirect-go-programs go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-baltica + (package + (name "python-baltica") + (version "1.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dieterich-lab/Baltica") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) + (build-system pyproject-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda _ + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively ".tests" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest" "-v" "--doctest-modules"))))))) + (propagated-inputs (list python-anndata + python-click + python-flask + python-flask-wtf + gunicorn + python-h5py + python-pysam + python-numpy + python-psutil + python-pyyaml + python-scipy + snakemake-7)) + (native-inputs (list python-pytest python-pyfakefs python-cython)) + (home-page "https://github.com/dieterich-lab/Baltica") + (synopsis "Integrated splice junction usage analysis") + (description + "This framework facilitates the execution of differential junction usage methods. +Additionally, it enables the integration of results from multiple DJU methods.") + (license license:expat))) + (define-public python-bamnostic (package (name "python-bamnostic") base-commit: 34b56974dfe720e5e30f04409ac216747d7e3f5c -- 2.34.1 ------------=_1690959001-3000-1--