diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 56 |
1 files changed, 54 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 773b5909b6..8d2cb93c7c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3693,6 +3693,58 @@ for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.") (license license:gpl2+))) +(define-public proteinortho + (package + (name "proteinortho") + (version "5.15") + (source + (origin + (method url-fetch) + (uri + (string-append + "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" + version "_src.tar.gz")) + (sha256 + (base32 + "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (replace 'configure + ;; There is no configure script, so we modify the Makefile directly. + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("INSTALLDIR=.*") + (string-append + "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) + #t)) + (add-before 'install 'make-install-directory + ;; The install directory is not created during 'make install'. + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) + #t)) + (add-after 'install 'wrap-programs + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((path (getenv "PATH")) + (out (assoc-ref outputs "out")) + (binary (string-append out "/bin/proteinortho5.pl"))) + (wrap-program binary `("PATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("perl" ,perl) + ("python" ,python-2) + ("blast+" ,blast+))) + (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") + (synopsis "Detect orthologous genes across species") + (description + "Proteinortho is a tool to detect orthologous genes across different +species. For doing so, it compares similarities of given gene sequences and +clusters them to find significant groups. The algorithm was designed to handle +large-scale data and can be applied to hundreds of species at once.") + (license license:gpl2+))) + (define-public pyicoteo (package (name "pyicoteo") @@ -3765,7 +3817,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.6.8") + (version "3.7.0") (source (origin (method url-fetch) @@ -3774,7 +3826,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw")))) + "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43")))) (build-system perl-build-system) (arguments `(#:phases |