bioconductor: Add r-rbioformats.

* guix-science/packages/bioconductor.scm (r-rbioformats): New variable.

1 files changed, 74 insertions, 0 deletions

diff --git a/guix-science/packages/bioconductor.scm b/guix-science/packages/bioconductor.scm
index f22c492..9123ddf 100644
--- a/guix-science/packages/bioconductor.scm
+++ b/guix-science/packages/bioconductor.scm
@@ -23,8 +23,10 @@
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
   #:use-module (gnu packages bioconductor)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
   #:use-module (guix-science packages cran)
+  #:use-module (gnu packages java)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
 
@@ -131,3 +133,75 @@ classes.  Special attention is given to single-cell data in a
 @code{SingleCellExperiment} object with visualization of
 dimensionality reduction results.")
     (license license:expat)))
+
+(define-public r-rbioformats
+  (package
+    (name "r-rbioformats")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RBioFormats" version))
+       (sha256
+        (base32 "0vqpr5g6v96gnfpznx09pwzcj4n2230hqh8hiip3m3pbnxicilnx"))
+       (snippet '(delete-file "inst/java/RBioFormats.jar"))))
+    (properties `((upstream-name . "RBioFormats")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:modules
+      '((guix build r-build-system)
+        ((guix build ant-build-system) #:prefix ant:)
+        (guix build utils))
+      #:imported-modules
+      `((guix build ant-build-system)
+        ,@%r-build-system-modules)
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'build-jar
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((jar (assoc-ref inputs "bioformats_package.jar")))
+                (with-directory-excursion "java"
+                  (mkdir "build")
+                  (invoke "javac" "-d" "./build" "-cp" jar
+                          "RBioFormats.java")
+                  (with-directory-excursion "build"
+                    (apply invoke "jar" "cvf" "../../inst/java/RBioFormats.jar"
+                           (find-files ".")))))))
+          (add-after 'install 'strip-jar-timestamps
+            (assoc-ref ant:%standard-phases 'strip-jar-timestamps))
+          (add-after 'unpack 'fix-jar-location
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((jar (assoc-ref inputs "bioformats_package.jar"))
+                    (target (string-append #$output "/share/bioformats_package_7.3.0.jar")))
+                (mkdir-p (dirname target))
+                (copy-file jar target)
+                (substitute* "R/zzz.R"
+                  (("cache_dir <-" m)
+                   (string-append "if (file.exists(file.path(\"" (dirname target)
+                                  "\", jar_filename))) { return(file.path(\""
+                                  (dirname target) "\", \""
+                                  (basename target) "\")); }\n"
+                                  m))))))
+          (add-after 'unpack 'fix-tests
+            (lambda _
+              (substitute* "tests/testthat/test-utils.R"
+                (("6") "7")))))))
+    (inputs (list (list openjdk11 "jdk")))
+    (propagated-inputs (list r-ebimage r-rjava r-s4vectors))
+    (native-inputs
+     (list r-knitr
+           r-testthat
+           zip
+           (origin
+             (method url-fetch)
+             ;; The exact version is mentioned in DESCRIPTION.
+             (uri "https://github.com/ome/bioformats/releases/download/v7.3.0/bioformats_package.jar")
+             (sha256
+              (base32 "11bagd1jydc0alv609q48b6xxrysqb7mk3kvq2rypgnvyfzdgcib")))))
+    (home-page "https://github.com/aoles/RBioFormats")
+    (synopsis "R interface to Bio-Formats")
+    (description
+     "This is an R package which interfaces with the OME Bio-Formats Java
+library to allow reading of proprietary microscopy image data and metadata.")
+    (license license:gpl3)))