From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add idr. Date: Wed, 17 Jun 2015 12:51:42 +0200 Message-ID: References: <87h9q7u0kn.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58910) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z5Awm-0002MX-PW for guix-devel@gnu.org; Wed, 17 Jun 2015 06:51:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z5Awg-00012d-LX for guix-devel@gnu.org; Wed, 17 Jun 2015 06:51:56 -0400 In-Reply-To: <87h9q7u0kn.fsf@gnu.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ludovic =?utf-8?Q?Court=C3=A8s?= Cc: guix-devel --=-=-= Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Ludovic Court=C3=A8s writes: >> + 'install 'wrap-program >> + (lambda* (#:key outputs #:allow-other-keys) >> + (let ((out (assoc-ref %outputs "out")) >> + (path (getenv "PYTHONPATH"))) >> + (wrap-program (string-append out "/bin/idr") >> + `("PYTHONPATH" ":" prefix (,path)))) > > Taking $PYTHONPATH as is has the effect of keeping a reference to Cytho= n > and to setuptools, which may not be what you want, given that they are > listed as =E2=80=98native-inputs=E2=80=99. > > Should it instead explicitly list SciPy, NumPy, and Matplotlib? You are right. Is the attached patch better? --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-idr.patch" >From 37db5b51fe4a09496e149d59b64aa0b69ae42fd1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 16 Jun 2015 11:33:26 +0200 Subject: [PATCH] gnu: Add idr. * gnu/packages/bioinformatics.scm (idr): New variable. --- gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb15d40..f243904 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1061,6 +1061,56 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public idr + (package + (name "idr") + (version "2.0.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/nboley/idr/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after + 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (python-version (string-take (string-take-right + (assoc-ref inputs "python") 5) 3)) + (path (string-join + (map (lambda (name) + (string-append (assoc-ref inputs name) + "/lib/python" python-version + "/site-packages")) + '("python-scipy" + "python-numpy" + "python-matplotlib")) + ":"))) + (wrap-program (string-append out "/bin/idr") + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-matplotlib" ,python-matplotlib))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/nboley/idr") + (synopsis "Tool to measure the irreproducible discovery rate (IDR)") + (description + "The IDR (Irreproducible Discovery Rate) framework is a unified approach +to measure the reproducibility of findings identified from replicate +experiments and provide highly stable thresholds based on reproducibility.") + (license license:gpl3+))) + (define-public macs (package (name "macs") -- 2.1.0 --=-=-=--