diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 71 |
1 files changed, 71 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1334600af6..df627fbe48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages file) #:use-module (gnu packages java) #:use-module (gnu packages linux) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) @@ -438,6 +439,76 @@ multiple sequence alignments.") "CLIPper is a tool to define peaks in CLIP-seq datasets.") (license license:gpl2))) +(define-public couger + (package + (name "couger") + (version "1.8.2") + (source (origin + (method url-fetch) + (uri (string-append + "http://couger.oit.duke.edu/static/assets/COUGER" + version ".zip")) + (sha256 + (base32 + "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (copy-recursively "src" (string-append out "/src")) + (mkdir (string-append out "/bin")) + ;; Add "src" directory to module lookup path. + (substitute* "couger" + (("from argparse") + (string-append "import sys\nsys.path.append(\"" + out "\")\nfrom argparse"))) + (copy-file "couger" (string-append out "/bin/couger"))) + #t)) + (add-after + 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Make sure 'couger' runs with the correct PYTHONPATH. + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out "/bin/couger") + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("python" ,python-2) + ("python2-pillow" ,python2-pillow) + ("python2-numpy" ,python2-numpy) + ("python2-scipy" ,python2-scipy) + ("python2-matplotlib" ,python2-matplotlib))) + (propagated-inputs + `(("r" ,r) + ("libsvm" ,libsvm) + ("randomjungle" ,randomjungle))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://couger.oit.duke.edu") + (synopsis "Identify co-factors in sets of genomic regions") + (description + "COUGER can be applied to any two sets of genomic regions bound by +paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify +putative co-factors that provide specificity to each TF. The framework +determines the genomic targets uniquely-bound by each TF, and identifies a +small set of co-factors that best explain the in vivo binding differences +between the two TFs. + +COUGER uses classification algorithms (support vector machines and random +forests) with features that reflect the DNA binding specificities of putative +co-factors. The features are generated either from high-throughput TF-DNA +binding data (from protein binding microarray experiments), or from large +collections of DNA motifs.") + (license license:gpl3+))) + (define-public clustal-omega (package (name "clustal-omega") |