From unknown Sat Jun 21 10:44:48 2025 X-Loop: help-debbugs@gnu.org Subject: bug#27181: [PATCH] gnu: Add kaiju. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 Jun 2017 13:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 27181 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 27181@debbugs.gnu.org X-Debbugs-Original-To: guix-devel Received: via spool by submit@debbugs.gnu.org id=B.149632319715088 (code B ref -1); Thu, 01 Jun 2017 13:20:02 +0000 Received: (at submit) by debbugs.gnu.org; 1 Jun 2017 13:19:57 +0000 Received: from localhost ([127.0.0.1]:48749 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGQ17-0003vG-4K for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:57 -0400 Received: from eggs.gnu.org ([208.118.235.92]:52733) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGQ15-0003uz-Ja for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:56 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGQ0z-000568-Ba for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:50 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.5 required=5.0 tests=BAYES_05,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:58801) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dGQ0z-000561-80 for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:49 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:43687) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGQ0x-0002JE-WF for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGQ0u-00053I-Ra for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:47 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:55053) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGQ0u-00053E-OJ for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:44 -0400 Received: from [143.121.198.177] (port=45772 helo=cog147) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dGQ0u-00043t-6z for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:44 -0400 References: User-agent: mu4e 0.9.18; emacs 25.2.1 From: Roel Janssen In-reply-to: Date: Thu, 01 Jun 2017 15:19:41 +0200 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) 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: -5.0 (-----) --=-=-= Content-Type: text/plain Dear Guix, Here's a patch for kaiju. A C++ program without any dependencies, plus some additional scripts that need perl. Kind regards, Roel Janssen --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-gnu-Add-kaiju.patch >From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 1 Jun 2017 15:01:51 +0200 Subject: [PATCH] gnu: Add kaiju. * gnu/packages/bioinformatics (kaiju): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ec69f50..a8ad424 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3214,6 +3214,43 @@ data.") (supported-systems '("x86_64-linux")) (license license:bsd-3))) +(define-public kaiju + (package + (name "kaiju") + (version "1.5.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/bioinformatics-centre/kaiju/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'move-to-src-dir + (lambda _ (chdir "src") #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (chdir "..") + (copy-recursively "bin" bin) + (copy-recursively "util" bin))))))) + (inputs + `(("perl" ,perl))) + (home-page "http://kaiju.binf.ku.dk/") + (synopsis "Fast and sensitive taxonomic classification for metagenomics") + (description "Kaiju is a program for sensitive taxonomic classification +of high-throughput sequencing reads from metagenomic whole genome sequencing +experiments.") + (license license:gpl3+))) + (define-public macs (package (name "macs") -- 2.7.4 --=-=-=-- From unknown Sat Jun 21 10:44:48 2025 X-Loop: help-debbugs@gnu.org Subject: bug#27181: [PATCH] gnu: Add kaiju. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 Jun 2017 15:24:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 27181 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen Cc: 27181@debbugs.gnu.org Received: via spool by 27181-submit@debbugs.gnu.org id=B27181.14963305971782 (code B ref 27181); Thu, 01 Jun 2017 15:24:01 +0000 Received: (at 27181) by debbugs.gnu.org; 1 Jun 2017 15:23:17 +0000 Received: from localhost ([127.0.0.1]:49870 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGRwT-0000Sg-2s for submit@debbugs.gnu.org; Thu, 01 Jun 2017 11:23:17 -0400 Received: from eggs.gnu.org ([208.118.235.92]:34580) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGRwR-0000SU-U6 for 27181@debbugs.gnu.org; Thu, 01 Jun 2017 11:23:16 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGRwH-0006yx-R4 for 27181@debbugs.gnu.org; Thu, 01 Jun 2017 11:23:10 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56714) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGRwH-0006yh-Nw for 27181@debbugs.gnu.org; Thu, 01 Jun 2017 11:23:05 -0400 Received: from [193.50.110.69] (port=44658 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dGRwG-00012j-RQ; Thu, 01 Jun 2017 11:23:05 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 13 Prairial an 225 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Thu, 01 Jun 2017 17:23:01 +0200 In-Reply-To: (Roel Janssen's message of "Thu, 01 Jun 2017 15:19:41 +0200") Message-ID: <877f0vyboq.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) 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: -5.0 (-----) Hi Roel! Roel Janssen skribis: > From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Thu, 1 Jun 2017 15:01:51 +0200 > Subject: [PATCH] gnu: Add kaiju. > > * gnu/packages/bioinformatics (kaiju): New variable. [...] > + (modify-phases %standard-phases > + (delete 'configure) > + (add-before 'build 'move-to-src-dir > + (lambda _ (chdir "src") #t)) > + (replace 'install > + (lambda* (#:key inputs outputs #:allow-other-keys) > + (let ((bin (string-append (assoc-ref outputs "out") "/bin")= )) > + (mkdir-p bin) > + (chdir "..") > + (copy-recursively "bin" bin) > + (copy-recursively "util" bin))))))) Make sure to return #t at the end of the phase. Otherwise LGTM! Thanks, Ludo=E2=80=99. From unknown Sat Jun 21 10:44:48 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: Roel Janssen Subject: bug#27181: closed (Re: bug#27181: [PATCH] gnu: Add kaiju.) Message-ID: References: X-Gnu-PR-Message: they-closed 27181 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 27181@debbugs.gnu.org Date: Fri, 02 Jun 2017 11:43:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1496403782-8287-1" This is a multi-part message in MIME format... ------------=_1496403782-8287-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #27181: [PATCH] gnu: Add kaiju. 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 27181@debbugs.gnu.org. --=20 27181: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D27181 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1496403782-8287-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 27181-done) by debbugs.gnu.org; 2 Jun 2017 11:42:45 +0000 Received: from localhost ([127.0.0.1]:50616 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGkyb-00029B-A9 for submit@debbugs.gnu.org; Fri, 02 Jun 2017 07:42:45 -0400 Received: from eggs.gnu.org ([208.118.235.92]:50911) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGkyZ-00028y-Nr for 27181-done@debbugs.gnu.org; Fri, 02 Jun 2017 07:42:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGkyT-0002dY-Ou for 27181-done@debbugs.gnu.org; Fri, 02 Jun 2017 07:42:38 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:51732) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGkyO-0002c5-Fe; Fri, 02 Jun 2017 07:42:32 -0400 Received: from [143.121.198.177] (port=47068 helo=cog147) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dGkyN-0006z0-Sz; Fri, 02 Jun 2017 07:42:32 -0400 References: <877f0vyboq.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Roel Janssen To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#27181: [PATCH] gnu: Add kaiju. Message-ID: In-reply-to: <877f0vyboq.fsf@gnu.org> Date: Fri, 02 Jun 2017 13:42:22 +0200 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: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 27181-done Cc: 27181-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: -5.0 (-----) Ludovic Courtès writes: > Hi Roel! > > Roel Janssen skribis: > >> From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001 >> From: Roel Janssen >> Date: Thu, 1 Jun 2017 15:01:51 +0200 >> Subject: [PATCH] gnu: Add kaiju. >> >> * gnu/packages/bioinformatics (kaiju): New variable. > > [...] > >> + (modify-phases %standard-phases >> + (delete 'configure) >> + (add-before 'build 'move-to-src-dir >> + (lambda _ (chdir "src") #t)) >> + (replace 'install >> + (lambda* (#:key inputs outputs #:allow-other-keys) >> + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) >> + (mkdir-p bin) >> + (chdir "..") >> + (copy-recursively "bin" bin) >> + (copy-recursively "util" bin))))))) > > Make sure to return #t at the end of the phase. Otherwise LGTM! I added the #t to the end of the phase. Thanks Ludo’! Pushed in b9a601d9db3aa1bdb877c0ac5e7f53077ee56185. Kind regards, Roel Janssen ------------=_1496403782-8287-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 1 Jun 2017 13:19:57 +0000 Received: from localhost ([127.0.0.1]:48749 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGQ17-0003vG-4K for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:57 -0400 Received: from eggs.gnu.org ([208.118.235.92]:52733) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dGQ15-0003uz-Ja for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:56 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGQ0z-000568-Ba for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:50 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.5 required=5.0 tests=BAYES_05,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:58801) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dGQ0z-000561-80 for submit@debbugs.gnu.org; Thu, 01 Jun 2017 09:19:49 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:43687) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGQ0x-0002JE-WF for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGQ0u-00053I-Ra for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:47 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:55053) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGQ0u-00053E-OJ for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:44 -0400 Received: from [143.121.198.177] (port=45772 helo=cog147) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dGQ0u-00043t-6z for guix-patches@gnu.org; Thu, 01 Jun 2017 09:19:44 -0400 References: User-agent: mu4e 0.9.18; emacs 25.2.1 From: Roel Janssen To: guix-devel Subject: [PATCH] gnu: Add kaiju. In-reply-to: Date: Thu, 01 Jun 2017 15:19:41 +0200 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) 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: -5.0 (-----) --=-=-= Content-Type: text/plain Dear Guix, Here's a patch for kaiju. A C++ program without any dependencies, plus some additional scripts that need perl. Kind regards, Roel Janssen --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-gnu-Add-kaiju.patch >From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 1 Jun 2017 15:01:51 +0200 Subject: [PATCH] gnu: Add kaiju. * gnu/packages/bioinformatics (kaiju): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ec69f50..a8ad424 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3214,6 +3214,43 @@ data.") (supported-systems '("x86_64-linux")) (license license:bsd-3))) +(define-public kaiju + (package + (name "kaiju") + (version "1.5.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/bioinformatics-centre/kaiju/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'move-to-src-dir + (lambda _ (chdir "src") #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (chdir "..") + (copy-recursively "bin" bin) + (copy-recursively "util" bin))))))) + (inputs + `(("perl" ,perl))) + (home-page "http://kaiju.binf.ku.dk/") + (synopsis "Fast and sensitive taxonomic classification for metagenomics") + (description "Kaiju is a program for sensitive taxonomic classification +of high-throughput sequencing reads from metagenomic whole genome sequencing +experiments.") + (license license:gpl3+))) + (define-public macs (package (name "macs") -- 2.7.4 --=-=-=-- ------------=_1496403782-8287-1--