From unknown Fri Sep 12 01:59:05 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#35792 <35792@debbugs.gnu.org> To: bug#35792 <35792@debbugs.gnu.org> Subject: Status: [PATCH 0/7] Package freebayes Reply-To: bug#35792 <35792@debbugs.gnu.org> Date: Fri, 12 Sep 2025 08:59:05 +0000 retitle 35792 [PATCH 0/7] Package freebayes reassign 35792 guix-patches submitter 35792 Pierre Neidhardt severity 35792 normal tag 35792 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:25:59 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:25:59 +0000 Received: from localhost ([127.0.0.1]:32907 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS35r-0007qZ-Cx for submit@debbugs.gnu.org; Sat, 18 May 2019 13:25:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:33906) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS35p-0007qN-Mb for submit@debbugs.gnu.org; Sat, 18 May 2019 13:25:58 -0400 Received: from lists.gnu.org ([209.51.188.17]:48606) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS35k-0000Xn-J4 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:25:52 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48288) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS35j-0003pZ-Jr for guix-patches@gnu.org; Sat, 18 May 2019 13:25:52 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS35i-0000We-P4 for guix-patches@gnu.org; Sat, 18 May 2019 13:25:51 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:59885) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS35i-0000Uu-Ih for guix-patches@gnu.org; Sat, 18 May 2019 13:25:50 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id A2AE5240005 for ; Sat, 18 May 2019 17:25:43 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 0/7] Package freebayes Date: Sat, 18 May 2019 19:25:43 +0200 Message-Id: <20190518172543.6766-1-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) Mostly ready for merge except for the FreeBayes test which don't pass because we need grep with PCRE support. Pierre Neidhardt (7): gnu: Add tabixpp. gnu: Add smithwaterman. gnu: Add multichoose. gnu: Add fsom. gnu: Add fastahack. gnu: Add vcflib. gnu: Add freebayes. gnu/packages/bioinformatics.scm | 400 ++++++++++++++++++++++++++++++++ 1 file changed, 400 insertions(+) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:26:54 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:54 +0000 Received: from localhost ([127.0.0.1]:32914 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36j-0007sa-Nt for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:53 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34078) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s8-IF for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:35681) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36a-00018n-QA for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:45 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48421) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D5-BV for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-000161-1T for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:43045) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36X-00014t-RB for guix-patches@gnu.org; Sat, 18 May 2019 13:26:41 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id C9A3A24000E for ; Sat, 18 May 2019 17:26:40 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 1/7] gnu: Add tabixpp. Date: Sat, 18 May 2019 19:26:34 +0200 Message-Id: <20190518172640.7165-1-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172543.6766-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (tabixpp): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37f2001ea3..244741854d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14830,3 +14830,42 @@ ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, @code{ataqv}, examines aligned reads and reports some basic metrics.") (license license:gpl3+))) + +(define-public tabixpp + (package + (name "tabixpp") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8")))) + (build-system gnu-build-system) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; The build phase needs overriding the location of htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + "HTS_HEADERS=" ; No need to check for headers here. + (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "tabix++" bin))))))) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "C++ wrapper around tabix project") + (description "This is a C++ wrapper around the Tabix project which abstracts +some of the details of opening and jumping in tabix-indexed files.") + (license license:expat))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:26:54 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:54 +0000 Received: from localhost ([127.0.0.1]:32916 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sc-1s for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:54 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34077) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s7-I6 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:32860) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36a-00018Y-H4 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48418) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D4-8u for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-00016G-7N for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:41027) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-000157-10 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 04FEC240011 for ; Sat, 18 May 2019 17:26:40 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 2/7] gnu: Add smithwaterman. Date: Sat, 18 May 2019 19:26:35 +0200 Message-Id: <20190518172640.7165-2-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (smithwaterman): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 244741854d..1bf33853b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14869,3 +14869,33 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (description "This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) + +(define-public smithwaterman + ;; TODO: Upgrading smithwaterman breaks FreeBayes. + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/smithwaterman/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "smithwaterman" bin))))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "Implementation of the Smith-Waterman algorithm.") + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. + (license (list license:gpl2 license:expat))))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:26:55 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:55 +0000 Received: from localhost ([127.0.0.1]:32919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sk-ET for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34082) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s9-J3 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:47058) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36b-00019L-Eq for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:46 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48434) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D6-Vi for guix-patches@gnu.org; Sat, 18 May 2019 13:26:45 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-00016i-Io for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:50409) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015P-8B for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 3633224000A for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 3/7] gnu: Add multichoose. Date: Sat, 18 May 2019 19:26:36 +0200 Message-Id: <20190518172640.7165-3-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (multichoose): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1bf33853b0..3ff0f69f5e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14899,3 +14899,39 @@ some of the details of opening and jumping in tabix-indexed files.") (description "Implementation of the Smith-Waterman algorithm.") ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. (license (list license:gpl2 license:expat))))) + +(define-public multichoose + (package + (name "multichoose") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/multichoose/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs")))) + (build-system gnu-build-system) + (native-inputs + `(("python" ,python-2) + ("node" ,node))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + ;; TODO: There are Python modules for these programs too. + (install-file "multichoose" bin) + (install-file "multipermute" bin))))))) + (home-page "https://github.com/ekg/multichoose") + (synopsis "Efficient loopless multiset combination generation algorithm") + (description "This library implements an efficient loopless multiset +combination generation algorithm which is (approximately) described in +\"Loopless algorithms for generating permutations, combinations, and other +combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), +1973. (Algorithm 7.)") + (license license:expat))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:26:59 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:59 +0000 Received: from localhost ([127.0.0.1]:32924 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007tQ-4R for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34111) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sC-AZ for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:44228) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36d-0001B5-L2 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48461) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DN-FU for guix-patches@gnu.org; Sat, 18 May 2019 13:26:47 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017P-8u for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:58071) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015X-Ih for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 66210240012 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 4/7] gnu: Add fsom. Date: Sat, 18 May 2019 19:26:37 +0200 Message-Id: <20190518172640.7165-4-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (fsom): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ff0f69f5e..e018b51968 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14935,3 +14935,32 @@ combination generation algorithm which is (approximately) described in combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)") (license license:expat))) + +(define-public fsom + (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3")) + (package + (name "fsom") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fsom/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "fsom" bin))))))) + (home-page "https://github.com/ekg/fsom") + (synopsis "Manage SOM (Self-Organizing Maps) neural networks") + (description "A tiny C library for managing SOM (Self-Organizing Maps) +neural networks.") + (license license:gpl3)))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:26:59 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:59 +0000 Received: from localhost ([127.0.0.1]:32926 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007tS-Fx for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34112) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sD-Lc for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:49996) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36d-0001BC-QB for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48463) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DO-G4 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:47 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017K-8L for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:38251) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015f-KN for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 91B17240013 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 5/7] gnu: Add fastahack. Date: Sat, 18 May 2019 19:26:38 +0200 Message-Id: <20190518172640.7165-5-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (fastahack): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e018b51968..3ad0a2a421 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14964,3 +14964,35 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), (description "A tiny C library for managing SOM (Self-Organizing Maps) neural networks.") (license license:gpl3)))) + +(define-public fastahack + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) + (package + (name "fastahack") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fastahack/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "fastahack" bin))))))) + (home-page "https://github.com/ekg/fastahack") + (synopsis "Indexing and sequence extraction from FASTA files") + (description "Fastahack is a small application for indexing and +extracting sequences and subsequences from FASTA files. The included library +provides a FASTA reader and indexer that can be embedded into applications +which would benefit from directly reading subsequences from FASTA files. The +library automatically handles index file generation and use.") + (license (list license:expat license:gpl2))))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:27:00 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:27:00 +0000 Received: from localhost ([127.0.0.1]:32928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007ta-Ol for submit@debbugs.gnu.org; Sat, 18 May 2019 13:27:00 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34113) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sE-M2 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:57655) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36e-0001BU-5Q for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48468) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DP-Gk for guix-patches@gnu.org; Sat, 18 May 2019 13:26:48 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017m-LW for guix-patches@gnu.org; Sat, 18 May 2019 13:26:45 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:35443) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Z-00015x-2e for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id C14E724000F for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 6/7] gnu: Add vcflib. Date: Sat, 18 May 2019 19:26:39 +0200 Message-Id: <20190518172640.7165-6-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (vcflib): New variable. --- gnu/packages/bioinformatics.scm | 107 ++++++++++++++++++++++++++++++++ 1 file changed, 107 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ad0a2a421..665c807de9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14870,6 +14870,24 @@ might be caused by ATAC-seq library prep or sequencing. The main program, some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define tabixpp-freebayes + ;; This version works with FreeBayes while the released + ;; version doesn't. The released creates a variable with the name \"vcf\" + ;; somewhere, which is also the name of a namespace in vcflib. + (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) + (package + (inherit tabixpp) + (name "tabixpp-freebayes") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) + (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -14996,3 +15014,92 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) + +(define-public vcflib + (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" )) + (package + (name "vcflib") + (version (git-version "1.0.2" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) + (build-system gnu-build-system) + (native-inputs + `(("zlib" ,zlib) + ;; Submodules. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src.tar.gz") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "fastahack") + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "multichoose-src" "multichoose") + (unpack "smithwaterman-src" "smithwaterman") + (unpack "tabixpp-src" "tabixpp"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("Makefile") + (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "tabixpp" + (invoke "make")) + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + ;; "-I" (assoc-ref inputs "htslib") "/include " + "\"") + "all"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")) + ;; The header files in src/ do not interface libvcflib, + ;; therefore they are left out. + (install-file "libvcflib.a" lib))))))) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 13:27:00 2019 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:27:00 +0000 Received: from localhost ([127.0.0.1]:32930 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36q-0007th-68 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:27:00 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34114) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sF-Mm for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:49448) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36e-0001Bb-AH for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48469) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DQ-Gt for guix-patches@gnu.org; Sat, 18 May 2019 13:26:48 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_LOW autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017t-P3 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:46 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:43661) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Z-00016C-6A for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id F2E6F240014 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt To: guix-patches@gnu.org Subject: [PATCH 7/7] gnu: Add freebayes. Date: Sat, 18 May 2019 19:26:40 +0200 Message-Id: <20190518172640.7165-7-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 217.70.183.193 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: -1.1 (-) X-Debbugs-Envelope-To: submit 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: -2.1 (--) * gnu/packages/bioinformatics.scm (freebayes): New variable. --- gnu/packages/bioinformatics.scm | 127 ++++++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 665c807de9..704db184eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15103,3 +15103,130 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) + +(define-public freebayes + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") + (revision "1") + (version "1.0.2")) + (package + (name "freebayes") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/freebayes.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("htslib" ,htslib))) + (native-inputs + `(("bc" ,bc) ; Needed for running tests. + ("samtools" ,samtools) ; Needed for running tests. + ("parallel" ,parallel) ; Needed for running tests. + ("procps" ,procps) ; Needed for running tests. + ("bamtools" ,bamtools) + ("bamtools" ,bamtools) + ("vcflib-src" ,(package-source vcflib)) + ;; These are submodules for the vcflib version used in freebayes. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ekg/intervaltree/archive/" + "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) + (file-name "intervaltree-src.tar.gz") + (sha256 + (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) + ;; These submodules are needed to run the tests. + ("bash-tap-src" ,(package-source bash-tap)) + ("test-simple-bash-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ingydotnet/test-simple-bash/") + (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) + (file-name "test-simple-bash-src.tar.gz") + (sha256 + (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) + (arguments + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "vcflib-src" "vcflib") + (unpack "fastahack-src" "vcflib/fastahack") + (unpack "filevercmp-src" "vcflib/filevercmp") + (unpack "fsom-src" "vcflib/fsom") + (unpack "intervaltree-src" "vcflib/intervaltree") + (unpack "multichoose-src" "vcflib/multichoose") + (unpack "smithwaterman-src" "vcflib/smithwaterman") + (unpack "tabixpp-src" "vcflib/tabixpp") + (unpack "test-simple-bash-src" "test/test-simple-bash") + (unpack "bash-tap-src" "test/bash-tap"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "vcflib" + (with-directory-excursion "tabixpp" + (pk "Compile tabixpp before compiling the main project.") + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" "HTS_HEADERS=" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) + (pk "Compile vcflib before compiling the main project.") + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") + "all")) + (pk "Compile the main project.") + (with-directory-excursion "src" + (substitute* "Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) + (invoke "make" + (string-append "BAMTOOLS_ROOT=" + (assoc-ref inputs "bamtools")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "bin/freebayes" bin) + (install-file "bin/bamleftalign" bin)))) + ;; TODO: There are three tests that fail. All because of the -P + ;; (--perl-regexp) option in grep, which is not compiled into the + ;; version of grep in Guix. + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "make" "test"))))))) + (home-page "https://github.com/ekg/freebayes") + (synopsis "Haplotype-based variant detector") + (description "FreeBayes is a Bayesian genetic variant detector designed to +find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), +indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and +complex events (composite insertion and substitution events) smaller than the +length of a short-read sequencing alignment.") + (license license:expat)))) -- 2.21.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 01 10:38:43 2019 Received: (at 35792) by debbugs.gnu.org; 1 Aug 2019 14:38:43 +0000 Received: from localhost ([127.0.0.1]:54857 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1htCE7-00053u-DI for submit@debbugs.gnu.org; Thu, 01 Aug 2019 10:38:43 -0400 Received: from mail.thebird.nl ([94.142.245.5]:41900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1htCE6-00053i-3U for 35792@debbugs.gnu.org; Thu, 01 Aug 2019 10:38:42 -0400 Received: by mail.thebird.nl (Postfix, from userid 1000) id 647061B65; Thu, 1 Aug 2019 16:38:35 +0200 (CEST) Date: Thu, 1 Aug 2019 09:38:35 -0500 From: Pjotr Prins To: Pierre Neidhardt Subject: Re: [bug#35792] [PATCH 7/7] gnu: Add freebayes. Message-ID: <20190801143835.nf35dhemsgqmvdut@thebird.nl> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> <20190518172640.7165-7-mail@ambrevar.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20190518172640.7165-7-mail@ambrevar.xyz> User-Agent: NeoMutt/20170113 (1.7.2) X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35792 Cc: 35792@debbugs.gnu.org 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 (-) Can someone push this? On Sat, May 18, 2019 at 07:26:40PM +0200, Pierre Neidhardt wrote: > * gnu/packages/bioinformatics.scm (freebayes): New variable. > --- > gnu/packages/bioinformatics.scm | 127 ++++++++++++++++++++++++++++++++ > 1 file changed, 127 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 665c807de9..704db184eb 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -15103,3 +15103,130 @@ and operating on records of genomic variation as it can be described by the VCF > format, and a collection of command-line utilities for executing complex > manipulations on VCF files.") > (license license:expat)))) > + > +(define-public freebayes > + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") > + (revision "1") > + (version "1.0.2")) > + (package > + (name "freebayes") > + (version (git-version version revision commit)) > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/ekg/freebayes.git") > + (commit commit))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) > + (build-system gnu-build-system) > + (inputs > + `(("zlib" ,zlib) > + ("htslib" ,htslib))) > + (native-inputs > + `(("bc" ,bc) ; Needed for running tests. > + ("samtools" ,samtools) ; Needed for running tests. > + ("parallel" ,parallel) ; Needed for running tests. > + ("procps" ,procps) ; Needed for running tests. > + ("bamtools" ,bamtools) > + ("bamtools" ,bamtools) > + ("vcflib-src" ,(package-source vcflib)) > + ;; These are submodules for the vcflib version used in freebayes. > + ;; This package builds against the .o files so we need to extract the source. > + ("tabixpp-src" ,(package-source tabixpp-freebayes)) > + ("smithwaterman-src" ,(package-source smithwaterman)) > + ("multichoose-src" ,(package-source multichoose)) > + ("fsom-src" ,(package-source fsom)) > + ("filevercmp-src" ,(package-source filevercmp)) > + ("fastahack-src" ,(package-source fastahack)) > + ("intervaltree-src" > + ,(origin > + (method url-fetch) > + (uri (string-append > + "https://github.com/ekg/intervaltree/archive/" > + "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) > + (file-name "intervaltree-src.tar.gz") > + (sha256 > + (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) > + ;; These submodules are needed to run the tests. > + ("bash-tap-src" ,(package-source bash-tap)) > + ("test-simple-bash-src" > + ,(origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/ingydotnet/test-simple-bash/") > + (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) > + (file-name "test-simple-bash-src.tar.gz") > + (sha256 > + (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) > + (arguments > + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. > + #:phases > + (modify-phases %standard-phases > + (delete 'configure) > + (add-after 'unpack 'unpack-submodule-sources > + (lambda* (#:key inputs #:allow-other-keys) > + (let ((unpack (lambda (source target) > + (with-directory-excursion target > + (if (file-is-directory? (assoc-ref inputs source)) > + (copy-recursively (assoc-ref inputs source) ".") > + (invoke "tar" "xvf" > + (assoc-ref inputs source) > + "--strip-components=1")))))) > + (and > + (unpack "vcflib-src" "vcflib") > + (unpack "fastahack-src" "vcflib/fastahack") > + (unpack "filevercmp-src" "vcflib/filevercmp") > + (unpack "fsom-src" "vcflib/fsom") > + (unpack "intervaltree-src" "vcflib/intervaltree") > + (unpack "multichoose-src" "vcflib/multichoose") > + (unpack "smithwaterman-src" "vcflib/smithwaterman") > + (unpack "tabixpp-src" "vcflib/tabixpp") > + (unpack "test-simple-bash-src" "test/test-simple-bash") > + (unpack "bash-tap-src" "test/bash-tap"))))) > + (add-after 'unpack-submodule-sources 'fix-makefile > + (lambda* (#:key inputs #:allow-other-keys) > + ;; We don't have the .git folder to get the version tag from. > + (substitute* '("vcflib/Makefile") > + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) > + (replace 'build > + (lambda* (#:key inputs make-flags #:allow-other-keys) > + (with-directory-excursion "vcflib" > + (with-directory-excursion "tabixpp" > + (pk "Compile tabixpp before compiling the main project.") > + (let ((htslib-ref (assoc-ref inputs "htslib"))) > + (invoke "make" "HTS_HEADERS=" > + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") > + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) > + (pk "Compile vcflib before compiling the main project.") > + (invoke "make" "CC=gcc" > + (string-append "CFLAGS=\"" "-Itabixpp " > + "-I" (assoc-ref inputs "htslib") "/include " "\"") > + "all")) > + (pk "Compile the main project.") > + (with-directory-excursion "src" > + (substitute* "Makefile" > + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) > + (invoke "make" > + (string-append "BAMTOOLS_ROOT=" > + (assoc-ref inputs "bamtools")))))) > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) > + (install-file "bin/freebayes" bin) > + (install-file "bin/bamleftalign" bin)))) > + ;; TODO: There are three tests that fail. All because of the -P > + ;; (--perl-regexp) option in grep, which is not compiled into the > + ;; version of grep in Guix. > + (replace 'check > + (lambda* (#:key tests? #:allow-other-keys) > + (when tests? > + (invoke "make" "test"))))))) > + (home-page "https://github.com/ekg/freebayes") > + (synopsis "Haplotype-based variant detector") > + (description "FreeBayes is a Bayesian genetic variant detector designed to > +find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), > +indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and > +complex events (composite insertion and substitution events) smaller than the > +length of a short-read sequencing alignment.") > + (license license:expat)))) > -- > 2.21.0 > > > > From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 08 08:20:42 2019 Received: (at 35792-done) by debbugs.gnu.org; 8 Aug 2019 12:20:42 +0000 Received: from localhost ([127.0.0.1]:40079 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvhPO-00013N-HB for submit@debbugs.gnu.org; Thu, 08 Aug 2019 08:20:42 -0400 Received: from flashner.co.il ([178.62.234.194]:51904) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvhPM-000134-4V for 35792-done@debbugs.gnu.org; Thu, 08 Aug 2019 08:20:40 -0400 Received: from localhost (unknown [31.210.177.218]) by flashner.co.il (Postfix) with ESMTPSA id 0D263401EC; Thu, 8 Aug 2019 12:20:33 +0000 (UTC) Date: Thu, 8 Aug 2019 15:20:32 +0300 From: Efraim Flashner To: Pjotr Prins Subject: Re: [bug#35792] [PATCH 7/7] gnu: Add freebayes. Message-ID: <20190808122032.GE5507@E2140> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> <20190518172640.7165-7-mail@ambrevar.xyz> <20190801143835.nf35dhemsgqmvdut@thebird.nl> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="GV0iVqYguTV4Q9ER" Content-Disposition: inline In-Reply-To: <20190801143835.nf35dhemsgqmvdut@thebird.nl> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 User-Agent: Mutt/1.12.1 (2019-06-15) X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 35792-done Cc: Pierre Neidhardt , 35792-done@debbugs.gnu.org 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 (-) --GV0iVqYguTV4Q9ER Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable I pushed this patch series with a few changes. I see also that freebayes 1.3.1 came out in the meantime. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --GV0iVqYguTV4Q9ER Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAl1ME48ACgkQQarn3Mo9 g1EtNA/8ChCsRkVM1pGGF67m7TI1c0u3bsShpPOxAGf4iwS1djqXCpQ9n9PpVSgK dSZWVhapndnhLCxzfYhOpYOmZG332pBXaRY5xjEfd/F2EbFserZVWqZhnjdgNHDj Yt34QFKKzlAEXnA6z/YrY+7x/kl1XXHuytSIS27gndoLZlxQ91qrDLwcWK+azdgp eTyQEKPBswtNsRUMi8LlGOLa8BbxCrYowNbPfeq23hLEASRURLYB9PR9EX1MPJLS t/0U5aeCU+SGytoA5PW583MKUQQAKY4wnMJUxsgUrdsPW5srYNZ0xZ41gfdFoZFy O9mr4zCa9pDNQMfzPS+UhGBEcOLWb8WqrdyPnO3HrwuRAkCienFZ/PFtvttVeD2V fbZ+QT7x//9h0sRRlObCE6w6qNlbKCVDV+hYvGxllwjAxurdnQQhTxsCCnNNZIZI h4bS2999EX6Jj+LxhmLG4SRUsGmZ5IvMh+dqfm5Ah3LkzoTGGqIqM8J+TyquBP6Q Qvv1kHcWO8ZsO3dHyJl+1nd0XBvfFAQd2DzzYbq1VElT7jJYtWSisXguVwHtG+4k smqN6w1+5YJdupCeEbjjUrrihBDblfapGUGBIUQozVWdADdR5HuZErCWWBtL4/jO rkCiOttz7bUZfLI0XML8uY6fnMUKvO65f3/tUSUuLpmGPF4xoZY= =Ha0J -----END PGP SIGNATURE----- --GV0iVqYguTV4Q9ER-- From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 08 10:30:34 2019 Received: (at 35792) by debbugs.gnu.org; 8 Aug 2019 14:30:34 +0000 Received: from localhost ([127.0.0.1]:41557 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvjR3-0002SM-OQ for submit@debbugs.gnu.org; Thu, 08 Aug 2019 10:30:34 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21306) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvjR1-0002SB-LU for 35792@debbugs.gnu.org; Thu, 08 Aug 2019 10:30:32 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1565274628; cv=none; d=zoho.com; s=zohoarc; b=KaOuSECqTgdcurV1wkLTKn4TwCl2TOpUcp8Tw7uozGxXP2T6iBsp7a4tau7fCbwJWeLqmQ2CP0Gr3kmEa+j/l4uxxRUlav6D/kPdrRKPATbV6l93hv2/ohdc+FB8PF0jQ2uG1ReVzBuWvc/emdzTNh/AIPGrLV6lL0PE5x8F5iQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1565274628; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=3y5BlRAj104XsuvbZyb110LhZGCdjz6GhXv49hXuIZU=; b=ETaQ8X7ludNMVh5z6VdqkpTAeOShxl9olbFqDqP+H+rgpcvA5npaZEdyFkuXGIoykyAnS8x3QwTWqFj9kHpE9eJfkD7dF5kLpJgf4ufNnh5zzvi9HyOzh5ETSl+Ey7pSHHBD7v9WWxKYYDvlzhfBiuCSJuOrxjmopxs2a05yCU0= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1565274628; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=363; bh=3y5BlRAj104XsuvbZyb110LhZGCdjz6GhXv49hXuIZU=; b=cD5Zi7uQ8icGVkV1MCC0cAKDN8Jj1n+DmTmi89iC4ELwI7pmbUyF+OY4UCj/pveS BiGhqHkHa1e7ZOh8pdxuPOKI0Bo3fq+Q3yuxFDw8Z7p8CXkZQAQdRN9kymTZEyzFAB7 JTtlXHYgtKVR7zGRQj+jvAIT39KJ4InsjYs2+piw= Received: from localhost (141.80.247.250 [141.80.247.250]) by mx.zohomail.com with SMTPS id 1565274627895442.5062720687906; Thu, 8 Aug 2019 07:30:27 -0700 (PDT) References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> <20190518172640.7165-2-mail@ambrevar.xyz> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus To: Pierre Neidhardt , Efraim Flashner Subject: Re: [bug#35792] [PATCH 2/7] gnu: Add smithwaterman. In-reply-to: <20190518172640.7165-2-mail@ambrevar.xyz> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 08 Aug 2019 16:30:24 +0200 Message-ID: <87r25vwwzj.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35792 Cc: 35792@debbugs.gnu.org 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 (-) Pierre Neidhardt writes: > * gnu/packages/bioinformatics.scm (smithwaterman): New variable. [=E2=80=A6] > + ;; The licensing terms are unclear: https://github.com/ekg/smithwa= terman/issues/9. > + (license (list license:gpl2 license:expat))))) If the licensing terms are unclear we should not include this package. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 08 12:29:14 2019 Received: (at 35792) by debbugs.gnu.org; 8 Aug 2019 16:29:14 +0000 Received: from localhost ([127.0.0.1]:41626 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvlHu-0005mt-38 for submit@debbugs.gnu.org; Thu, 08 Aug 2019 12:29:14 -0400 Received: from flashner.co.il ([178.62.234.194]:52678) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvlHs-0005mf-Kt for 35792@debbugs.gnu.org; Thu, 08 Aug 2019 12:29:13 -0400 Received: from [192.168.1.242] (unknown [31.210.177.218]) by flashner.co.il (Postfix) with ESMTPSA id 6352B400F6; Thu, 8 Aug 2019 16:29:05 +0000 (UTC) Date: Thu, 08 Aug 2019 16:29:07 +0000 User-Agent: K-9 Mail for Android In-Reply-To: <87r25vwwzj.fsf@elephly.net> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> <20190518172640.7165-2-mail@ambrevar.xyz> <87r25vwwzj.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Subject: Re: [bug#35792] [PATCH 2/7] gnu: Add smithwaterman. To: Ricardo Wurmus ,Pierre Neidhardt From: Efraim Flashner Message-ID: X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 35792 Cc: 35792@debbugs.gnu.org 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 (-) https://github=2Ecom/ekg/smithwaterman/issues/9#issuecomment-493694384 Between the two licenses it's GPL2=2E The expat license text just hasn't b= een removed=2E On August 8, 2019 2:30:24 PM UTC, Ricardo Wurmus wr= ote: > >Pierre Neidhardt writes: > >> * gnu/packages/bioinformatics=2Escm (smithwaterman): New variable=2E >[=E2=80=A6] >> + ;; The licensing terms are unclear: >https://github=2Ecom/ekg/smithwaterman/issues/9=2E >> + (license (list license:gpl2 license:expat))))) > >If the licensing terms are unclear we should not include this package=2E > >-- >Ricardo --=20 Sent from my Android device with K-9 Mail=2E Please excuse my brevity=2E From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 08 12:31:46 2019 Received: (at 35792) by debbugs.gnu.org; 8 Aug 2019 16:31:47 +0000 Received: from localhost ([127.0.0.1]:41630 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvlKM-0005tR-IN for submit@debbugs.gnu.org; Thu, 08 Aug 2019 12:31:46 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21373) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hvlKK-0005tD-IT for 35792@debbugs.gnu.org; Thu, 08 Aug 2019 12:31:45 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1565281896; cv=none; d=zoho.com; s=zohoarc; b=In2ZCG18/1BMTDnP3sZWNUiMxkonAvP56wyabFQVTZCUjdNGnet4vDjkWd6nOxugt1p84jUaV3jrF3Jn0zuvLVqhpE5RWz0Yprv+bkjQRCF4hHmV5CLVDmL8VZ2yyixfdPvdTHx7PM9u1T15XgNe1/NYi7yjRUgE2TGVcy0XWo8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1565281896; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=ImBNdeXGa4tSuKgfbCWiU9LHQmLEtJexrdL31NK3fMw=; b=I+p7qiPqrWyLyG50Q0X3oqqk7QQer1xxSuX4NIxcgQrhKCD7jKkc7eszpm9EAP+DtznqCyrQA7oOsDEj1Ri5SsKhyR5tr9Afx1vGafzeqk87V59xP90WRSw2DbiBgV0oXk0XDZc5ZVH6N/DAAJ4VWTbTP4P2fTnU05KWSIzgGIQ= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1565281896; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type; l=258; bh=ImBNdeXGa4tSuKgfbCWiU9LHQmLEtJexrdL31NK3fMw=; b=E7UeWdTLAkTI6X636PWVk+jLqWMkY6Qb2HETjj3ioeIwYfTRKJlVlkSsDw2LfhuJ iEVw02q4y5Lj8Au6GmCTO60127DMA9c18yrujBQA/n6uj5r73iYEK86+KqlxiuYxmJC PgmkjqceWzvpED1YeJdb/hkk+tZDoKM5CwIE1I8o= Received: from localhost (141.80.247.250 [141.80.247.250]) by mx.zohomail.com with SMTPS id 1565281895438173.48241224118453; Thu, 8 Aug 2019 09:31:35 -0700 (PDT) References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> <20190518172640.7165-2-mail@ambrevar.xyz> <87r25vwwzj.fsf@elephly.net> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus To: Efraim Flashner Subject: Re: [bug#35792] [PATCH 2/7] gnu: Add smithwaterman. In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 08 Aug 2019 18:31:32 +0200 Message-ID: <87lfw3wrdn.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 35792 Cc: Pierre Neidhardt , 35792@debbugs.gnu.org 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 (-) Efraim Flashner writes: > https://github.com/ekg/smithwaterman/issues/9#issuecomment-493694384 > > Between the two licenses it's GPL2. The expat license text just hasn't been removed. Okay, that makes sense. -- Ricardo From unknown Fri Sep 12 01:59:05 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 06 Sep 2019 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator