From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Add express-beta-diversity Date: Thu, 15 Oct 2015 23:11:39 +1000 Message-ID: <561FA60B.3060404@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------090303090603000204080605" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37841) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZmiK0-0006cS-He for guix-devel@gnu.org; Thu, 15 Oct 2015 09:11:56 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZmiJv-0001u2-Gc for guix-devel@gnu.org; Thu, 15 Oct 2015 09:11:52 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:49622 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZmiJu-0001pI-TT for guix-devel@gnu.org; Thu, 15 Oct 2015 09:11:47 -0400 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: "guix-devel@gnu.org" , Donovan Parks This is a multi-part message in MIME format. --------------090303090603000204080605 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Hi, I noticed when packaging this that when "python" is provided as an input (and not python-2), then the python scripts don't get their shebangs fixed, because there is no python executable in the $PATH (it is python3). This seems not right to me - is there a reason for this, maybe so python 2 and 3 can coexist? In this case the python script was written with python-2 in mind so it doesn't matter here though. Thanks in advance for the review. ben --------------090303090603000204080605 Content-Type: text/x-patch; name="0001-gnu-Add-express-beta-diversity.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-express-beta-diversity.patch" >From 8d6f94c67df09e7830414fcf748da311a1167314 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 15 Oct 2015 22:53:31 +1000 Subject: [PATCH] gnu: Add express-beta-diversity. * gnu/packages/bioinformatics.scm (express-beta-diversity): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4b7f76b..8c2cbb1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1086,6 +1086,51 @@ analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.") (license license:artistic2.0))) +(define-public express-beta-diversity + (package + (name "express-beta-diversity") + (version "1.0.7") + (source (origin + (method url-fetch) + (uri + (string-append + "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) + (replace 'check + (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" + "-u")))) + (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "scripts/convertToEBD.py" + (string-append bin "/convertToEBD.py")) + (copy-file "bin/ExpressBetaDiversity" + (string-append bin "/ExpressBetaDiversity")) + #t)))))) + (inputs + `(("python" ,python-2))) + (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") + (synopsis "Taxon- and phylogenetic-based beta diversity measures") + (description + "Express Beta Diversity (EBD) calculates ecological beta diversity +(dissimilarity) measures between biological communities. EBD implements a +variety of diversity measures including those that make use of phylogenetic +similarity of community members.") + (license license:gpl3+))) + (define-public fasttree (package (name "fasttree") -- 2.4.3 --------------090303090603000204080605--