diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 90 |
1 files changed, 90 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 1011c7f..a362b73 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -66,6 +66,7 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages statistics) + #:use-module (gnu packages sqlite) #:use-module (gnu packages tcl) #:use-module (gnu packages time) #:use-module (gnu packages tls) @@ -2510,3 +2511,92 @@ procedure to recover optimal exons sets. It reduces redundancies in multiple discoveries of the same gene and resolves conflicting gene predictions on the same strand.") (license license:gpl3))) + +(define-public augustus + (package + (name "augustus") + (version "3.4.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Gaius-Augustus/Augustus") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1nc4nddcxi98fb14vmgj7x5aw5vglm4amzraqibgzmigpqnca68f")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list (string-append "CC=" ,(cc-for-target)) + (string-append "CXX=" ,(cxx-for-target))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ; No configure script + (add-after 'unpack 'adjust-sources + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "common.mk" + ;; Has the wrong version. + (("AUGVERSION = .*") + (string-append "AUGVERSION = " ,version "\n")) + ;; Looks for ancient version of mysql. + (("COMPGENEPRED = ") + "SQLITE=true\nMYSQL = false\nCOMPGENEPRED = ")) + (substitute* "src/Makefile" + (("/usr/include/lpsolve") + (string-append (assoc-ref inputs "lpsolve") "/include/lpsolve"))) + (substitute* (find-files "auxprogs" "Makefile") + (("/usr/include/bamtools") + (string-append (assoc-ref inputs "bamtools") "/include/bamtools")) + (("/usr/include/htslib") + (string-append (assoc-ref inputs "htslib") "/include/htslib")) + (("/usr/include/boost") + (string-append (assoc-ref inputs "boost") "/include/boost"))) + #t)) + (replace 'check + (lambda args + ;; These tests rely on mysql. + ;(apply (assoc-ref %standard-phases 'check) + ; `(,@args #:test-target "unit_test")) + (apply (assoc-ref %standard-phases 'check) + `(,@args #:test-target "test")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/augstus")) + (scripts (string-append share "/scripts"))) + ;; Install targets taken from Debian. + (install-file "auxprogs/bam2wig/bam2wig" bin) + (install-file "auxprogs/compileSpliceCands/compileSpliceCands" bin) + (install-file "auxprogs/homGeneMapping/src/homGeneMapping" bin) + (install-file "auxprogs/joingenes/joingenes" bin) + (mkdir-p scripts) + (copy-recursively "scripts" scripts) + (copy-recursively "config" share) + (with-directory-excursion "scripts" + (for-each delete-file (cons "executeTestCGP.py" + (find-files "." "\\.txt$")))) + (for-each make-file-writable (find-files out "\\.gz$")) + #t)))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("perl" ,perl) + ("python" ,python) + ("sqlite" ,sqlite) + ("zlib" ,zlib))) + (native-inputs + `(("bamtools" ,bamtools) + ("gsl" ,gsl) + ("gzip" ,gzip) + ("lpsolve" ,lpsolve) + ("samtools" ,samtools) + ("suitesparse" ,suitesparse))) + (home-page "http://bioinf.uni-greifswald.de/webaugustus/") + (synopsis "Genome annotation with AUGUSTUS") + (description "Augustus can be used as an ab initio program, which means it +bases its prediction purely on the sequence. AUGUSTUS may also incorporate +hints on the gene structure coming from extrinsic sources such as EST, MS/MS, +protein alignments and syntenic genomic alignments.") + (license (license:non-copyleft + "https://opensource.org/licenses/artistic-license-1.0" + "Artistic-license-1.0")))) |