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-rw-r--r--gn/packages/bioinformatics.scm90
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"))))