gnu: Add mageck.

* gnu/packages/bioinformatics.scm (mageck): New variable.

Change-Id: I0d232473c983ac98aa01ef39a96e938da8628b7d

gnu/packages/bioinformatics.scm

@@ -9780,6 +9780,97 @@ sequences).")
               "https://mafft.cbrc.jp/alignment/software/license.txt"
               "BSD-3 with different formatting"))))
 
+(define-public mageck
+  (package
+    (name "mageck")
+    (version "0.5.9.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/mageck/"
+                                  (version-major+minor version)
+                                  "/mageck-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0fnry7d3ngiw0jarvmwd3pxy5vvsf931m4aifz6mjfd6dl1ihsmh"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:modules '((guix build pyproject-build-system)
+                  (guix build utils)
+                  (srfi srfi-1)
+                  (ice-9 match))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'use-python3
+            (lambda _
+              (substitute* "bin/mageck"
+                (("python2") "python"))))
+         (add-after 'unpack 'numpy-compatibility
+           (lambda _
+              (substitute* "mageck/cnv_normalization.py"
+                (("np.float") "float"))))
+          ;; The build system declares executables both in "scripts" and
+          ;; "data", which all are supposed to end up in #$output/bin.  The
+          ;; pyproject-build-system gets confused by this, though, so we have
+          ;; to manually install the mageck executable after the 'install
+          ;; phase.
+          (add-after 'unpack 'patch-build-system
+            (lambda _
+              (substitute* "setup.py"
+                (("scripts=\\['bin/mageck'\\],") ""))))
+          (add-after 'install 'install-mageck
+            (lambda _
+              (install-file "bin/mageck" (string-append #$output "/bin"))))
+          (add-after 'install-mageck 'make-excutable
+            (lambda _
+              (for-each (lambda (file) (chmod file #o555))
+                        (find-files (string-append #$output "/bin")))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (let ((tests '(("demo1" "run.sh")
+                               ("demo2" "runmageck.sh")
+                               ("demo3" "run.sh")
+                               ("demo4" "run.sh"))))
+                  (setenv "PATH"
+                          (string-append #$output "/bin:"
+                                         (getenv "PATH")))
+                  (for-each (match-lambda
+                              ((dir script)
+                               (with-directory-excursion (string-append "demo/" dir)
+                                 (invoke "bash" script))))
+                            tests))))))))
+    (inputs
+     (list python-numpy
+           python-scipy
+           python-matplotlib
+           python-statsmodels
+           python-pyqt
+           r-minimal
+           r-xtable
+           r-gplots))
+    (home-page "https://sourceforge.net/projects/mageck/")
+    (synopsis "Model-based analysis of genome-wide CRISPR-Cas9 Knockout")
+    (description
+     "Model-based Analysis of Genome-wide CRISPR-Cas9
+Knockout (MAGeCK) is a computational tool to identify important genes
+from the recent genome-scale CRISPR-Cas9 knockout screens
+technology.  Its features include:
+
+@enumerate
+@item Simple, easy to use pipeline to screen genes in Genome-wide
+   CRISPR-Cas9 Knockout experiments;
+@item High sensitivity and low false discovery rate;
+@item Fully utilize the screening data by performing both positive and
+   negative screening in one dataset;
+@item Provide statistical evaluation in genes, sgRNAs and pathways;
+@item Require as few as 2 samples;
+@item Identify cell-type specific targets;
+@item A set of visualization features that generate publication
+   standard figures.
+@end enumerate\n")
+    (license license:bsd-3)))
+
 (define-public mash
   (package
     (name "mash")