From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add MAFFT. Date: Sun, 26 Jul 2015 13:10:14 +1000 Message-ID: <55B44F96.8050808@uq.edu.au> References: <55B0E173.1030406@uq.edu.au> <876158xcoo.fsf@mdc-berlin.de> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------000609020404020902060101" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35600) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZJCKc-0001eN-En for guix-devel@gnu.org; Sat, 25 Jul 2015 23:10:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZJCKZ-0008I8-5X for guix-devel@gnu.org; Sat, 25 Jul 2015 23:10:30 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:58348 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZJCKY-0008G6-C0 for guix-devel@gnu.org; Sat, 25 Jul 2015 23:10:26 -0400 In-Reply-To: <876158xcoo.fsf@mdc-berlin.de> 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: Ricardo Wurmus Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------000609020404020902060101 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id t6Q3AGpB022866 On 26/07/15 05:26, Ricardo Wurmus wrote: > Hi Ben, > >> + #:phases >> + (modify-phases %standard-phases >> + (add-after 'unpack 'enter-dir >> + (lambda _ (chdir "core") #t)) >> + ;; on advice from the MAFFT authors, do not distribute mafft= -profile, >> + ;; mafft-distance mafft-homologs.rb > What does this mean? Are they non-free software? If so, they should b= e > removed in a snippet. Sorry for the confusion. MAFFT itself is all free software, but on the=20 website it allows you to download a version "with-extensions" which=20 includes non-free software. I contacted the MAFFT authors and they suggested that there was no need=20 to distribute these three programs in a mafft package. I've updated the=20 comment to clarify. I'm actually a bit confused as to the difference between a snippet vs. a=20 patch stage as above - when is each appropriate? Snippets are only for=20 removing non-free software? > >> + (add-after 'enter-dir 'patch-makefile >> + (lambda _ >> + (substitute* "Makefile" >> + (("^SCRIPTS =3D mafft mafft-homologs.rb") >> + "SCRIPTS =3D mafft") >> + (((string-append "^PROGS =3D dvtditr dndfast7= dndblast" >> + " sextet5 mafft-distance")) >> + "PROGS =3D dvtditr dndfast7 dndblast sextet5= ") >> + (((string-append "splittbfast disttbfast tbfa= st " >> + "mafft-profile f2cl mccaskil= lwrap")) >> + "splittbfast disttbfast tbfast f2cl mccaskil= lwrap") > This line looks particularly unclear. It took me a little too long to > find the difference in the replacement. Is there a nicer regular > expression that you could use to indicate the removal of > =E2=80=9Cmafft-profile=E2=80=9D? I've added comments and alignment. ben --------------000609020404020902060101 Content-Type: text/x-patch; name="0001-gnu-Add-mafft.patch" Content-Disposition: attachment; filename="0001-gnu-Add-mafft.patch" Content-Transfer-Encoding: 7bit >From ce50d7382c8f7f092faa56ff5316134417a9eca1 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 26 Jul 2015 13:01:01 +1000 Subject: [PATCH] gnu: Add mafft. * gnu/packages/bioinformatics.scm (mafft): New variable --- gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++---- 1 file changed, 54 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38f01a8..11ef454 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -54,6 +54,54 @@ #:use-module (gnu packages xml) #:use-module (gnu packages zip)) +(define-public aragorn + (package + (name "aragorn") + (version "1.2.36") + (source (origin + (method url-fetch) + (uri (string-append + "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" + version ".tgz")) + (sha256 + (base32 + "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (zero? (system* "gcc" + "-O3" + "-ffast-math" + "-finline-functions" + "-o" + "aragorn" + (string-append "aragorn" ,version ".c"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (mkdir-p bin) + (copy-file "aragorn" + (string-append bin "/aragorn")) + (mkdir-p man) + (copy-file "aragorn.1" + (string-append man "/aragorn.1"))) + #t))))) + (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") + (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") + (description + "Aragorn identifies transfer RNA, mitochondrial RNA and +transfer-messenger RNA from nucleotide sequences, based on homology to known +tRNA consensus sequences and RNA structure. It also outputs the secondary +structure of the predicted RNA.") + (license license:gpl2))) + (define-public bamtools (package (name "bamtools") @@ -148,7 +196,7 @@ computational cluster.") (define-public bedtools (package (name "bedtools") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" @@ -156,7 +204,7 @@ computational cluster.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl")))) + "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) (inputs `(("samtools" ,samtools) @@ -1409,7 +1457,7 @@ sequencing tag position and orientation.") "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no automated tests, though there are tests in the readme + `(#:tests? #f ; no automated tests, though there are tests in the read me #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) (string-append "BINDIR=" (string-append (assoc-ref %outputs "out") @@ -1424,10 +1472,11 @@ sequencing tag position and orientation.") ;; distribute mafft-profile, mafft-distance, or ;; mafft-homologs.rb as they are too "specialised". (substitute* "Makefile" + ;; remove mafft-homologs.rb from SCRIPTS (("^SCRIPTS = mafft mafft-homologs.rb") "SCRIPTS = mafft") - ;; remove mafft-distance from PROGS - (((string-append "^PROGS = dvtditr dndfast7 dndblast" + ;; remove mafft-distance from PROGS + (((string-append "^PROGS = dvtditr dndfast7 dndblast" " sextet5 mafft-distance")) "PROGS = dvtditr dndfast7 dndblast sextet5") ;; remove mafft-profile from PROGS -- 2.4.3 --------------000609020404020902060101--