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