From 91f6f758f40f3eeba656aa5fb7e9c1f67d38978f Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Tue, 23 Feb 2016 23:31:57 +0100
Subject: Latest Sambamba. Link failure.

---
 gn/packages/bioinformatics.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3363ea2..90da815 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -310,7 +310,9 @@ minimize the amount of work necessary.  Unlike make, rdmd tracks dependencies
 and freshness without requiring additional information from the user.")
       (license license:boost1.0))))
 
+
 (define-public sambamba
+  ;;(let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
   (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
     (package
       (name "sambamba")
@@ -319,11 +321,14 @@ and freshness without requiring additional information from the user.")
         (method git-fetch)
         (uri (git-reference                
               (url "https://github.com/pjotrp/sambamba.git")
+              ;;(url "https://github.com/roelj/sambamba.git")
               (commit commit)))
         (file-name (string-append name "-" version "-checkout"))
         (sha256
          (base32
-          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
+          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
+          ;;"14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"
+          ))))
       (build-system gnu-build-system)
       ;; (inputs
       ;;  `(("ldc" ,ldc)
@@ -395,7 +400,10 @@ and freshness without requiring additional information from the user.")
            (replace
             'build
             (lambda* (#:key inputs make-flags #:allow-other-keys)
-              (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2")))))))
+              (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc"
+                              "D_COMPILER=ldc2"
+                              (string-append "LDC_LIB_PATH="
+                                (assoc-ref inputs "ldc") "/lib"))))))))
       (home-page "https://github.com/lomereiter/sambamba")
       (synopsis "A tool for working with SAM and BAM files written in D.")
       (description
-- 
cgit v1.2.3


From 1f1521af21ccdad98ad60d3d7e60c0ba4f5eb1dd Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 24 Feb 2016 12:50:24 +0100
Subject: A working version for Sambamba.

---
 gn/packages/bioinformatics.scm | 69 ++++++++++++++----------------------------
 htslib-add-cram_to_bam.patch   | 27 +++++++++++++++++
 2 files changed, 50 insertions(+), 46 deletions(-)
 create mode 100644 htslib-add-cram_to_bam.patch

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 90da815..bf39935 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -310,9 +310,7 @@ minimize the amount of work necessary.  Unlike make, rdmd tracks dependencies
 and freshness without requiring additional information from the user.")
       (license license:boost1.0))))
 
-
 (define-public sambamba
-  ;;(let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
   (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
     (package
       (name "sambamba")
@@ -321,48 +319,29 @@ and freshness without requiring additional information from the user.")
         (method git-fetch)
         (uri (git-reference                
               (url "https://github.com/pjotrp/sambamba.git")
-              ;;(url "https://github.com/roelj/sambamba.git")
               (commit commit)))
         (file-name (string-append name "-" version "-checkout"))
         (sha256
          (base32
-          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
-          ;;"14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"
-          ))))
+          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
       (build-system gnu-build-system)
-      ;; (inputs
-      ;;  `(("ldc" ,ldc)
-      ;;    ;; These are currently included in "ldc".
-      ;;    ;;("druntime-ldc" ,druntime-ldc)
-      ;;    ;;("phobos2-ldc" ,phobos2-ldc)
-      ;;    ("lz4" ,lz4)))
       (native-inputs
        `(("ldc" ,ldc)
-         ;;("druntime-ldc" ,druntime-ldc)
-         ;;("phobos2-ldc" ,phobos2-ldc)
          ("lz4" ,lz4)
          ("rdmd" ,rdmd)
          ("zlib" ,zlib)
-         ("perl" ,perl) ; Needed for htslib
-         ("ruby" ,ruby) ; Needed for htslib
-         ("python" ,python) ; Needed for htslib
+         ("perl" ,perl) ; Needed for htslib tests?
+         ("ruby" ,ruby) ; Needed for htslib tests?
+         ("python" ,python) ; Needed for htslib tests?
          ("gcc" ,gcc)
-         ("lz4-src"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://github.com/Cyan4973/lz4/archive/r131.tar.gz"))
-             (file-name "lz4-r131.tar.gz")
-             (sha256
-              (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx"))))
          ("htslib-src"
           ,(origin
              (method url-fetch)
-             (uri (string-append
-                   "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
-             (file-name "htslib-0.2.0-rc10.tar.gz")
+             (uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
+             (file-name "htslib-1.3.tar.gz")
              (sha256
-              (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
+              (base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
+             (patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
          ("biod-src"
           ,(origin
              (method git-fetch)
@@ -374,36 +353,34 @@ and freshness without requiring additional information from the user.")
               (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))))))
       (arguments
        `(#:tests? #f
-         ;;#:make-flags 
+         #:make-flags (list "-f" "Makefile.guix")
          #:phases
          (modify-phases %standard-phases
            (delete 'configure)
            (delete 'check)
            (add-after 'unpack 'unpack-htslib-sources
              (lambda* (#:key inputs #:allow-other-keys)
-               ;; Unfortunately, the current build compiles htslib statically
-               ;; into the executable.  Instead of patching the build files
-               ;; for Guix, this should be resolved on Sambamba upstream.  For
-               ;; now, just extract the source code to the desired directory.
+               ;; The current build compiles htslib statically into the
+               ;; executable.  On top of that, we need to patch the latest
+               ;; version of htslib to have it working with Sambamba.
                (and (with-directory-excursion "htslib"
                       (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
                                       "--strip-components=1")))
-                    (with-directory-excursion "lz4"
-                      (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
-                                      "--strip-components=1")))
-                    (and (zero? (system* "rm" "-r" "BioD"))
-                         (zero? (system* "ln" "--symbolic" "--no-target-directory"
-                                         (assoc-ref inputs "biod-src") "BioD"))))))
-           ;; Building a production-quality executable is done with a
-           ;; non-default make target. Adding it with #:make-flags breaks
-           ;; building tests.  Therefore, the default make got replaced by this.
+                    (zero? (system* "rm" "-r" "BioD"))
+                    (zero? (system* "ln" "--symbolic" "--no-target-directory"
+                                    (assoc-ref inputs "biod-src") "BioD")))))
            (replace
             'build
             (lambda* (#:key inputs make-flags #:allow-other-keys)
-              (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc"
-                              "D_COMPILER=ldc2"
+              (zero? (system* "make" "-f" "Makefile.guix"
                               (string-append "LDC_LIB_PATH="
-                                (assoc-ref inputs "ldc") "/lib"))))))))
+                                             (assoc-ref inputs "ldc")
+                                             "/lib")))))
+           (replace
+            'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+                (install-file "build/sambamba" bin)))))))
       (home-page "https://github.com/lomereiter/sambamba")
       (synopsis "A tool for working with SAM and BAM files written in D.")
       (description
diff --git a/htslib-add-cram_to_bam.patch b/htslib-add-cram_to_bam.patch
new file mode 100644
index 0000000..8c43497
--- /dev/null
+++ b/htslib-add-cram_to_bam.patch
@@ -0,0 +1,27 @@
+This patch adds the cram_to_bam function to the public interface of htslib,
+because it is used by code in Sambamba.
+
+by Roel Janssen <roel@gnu.org>
+--- a/cram/cram_decode.c	2015-12-15 17:34:33.000000000 +0100
++++ b/cram/cram_decode.c	2016-02-24 11:16:10.491808702 +0100
+@@ -2730,7 +2730,7 @@
+  * Returns the used size of the bam record on success
+  *         -1 on failure.
+  */
+-static int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
++int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
+ 		       cram_record *cr, int rec, bam_seq_t **bam) {
+     int bam_idx, rg_len;
+     char name_a[1024], *name;
+diff -Naur htslib-1.3/cram/cram_decode.h htslib-1.3-patched/cram/cram_decode.h
+--- htslib-1.3/cram/cram_decode.h	2015-12-15 17:34:33.000000000 +0100
++++ htslib-1.3-patched/cram/cram_decode.h	2016-02-24 11:15:04.556809864 +0100
+@@ -104,6 +104,8 @@
+ int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
+ 		      SAM_hdr *hdr);
+ 
++int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
++                cram_record *cr, int rec, bam_seq_t **bam);
+ 
+ #ifdef __cplusplus
+ }
-- 
cgit v1.2.3


From 362952ac8741a7f44b8176de3e7b15fbb8fae0b1 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 25 Feb 2016 09:28:24 +0000
Subject: Add older version of python-pil

---
 gn/packages/python.scm | 86 +++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 71 insertions(+), 15 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8f2bc80..61d186b 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -357,23 +357,79 @@ project)")
   (description #f)
   (license #f)))
 
-(define-public python2-piddle
+(define-public python2-pil-1.1.6
   (package
-    (name "python2-piddle")
-    (version "1.0.15")
+    (name "python2-pil")
+    (version "1.1.6")
     (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             ;; http://sourceforge.net/projects/numpy/files/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz/download
-             "mirror://sourceforge/piddle/piddle-" version ".zip"
-             ))
-       ;; (file-name (string-append name "-" version ".zip"))
-       (sha256
-        (base32
-         "0jaxfsrcgqb5cf2wznxnpdws5khlrdixmg85lrhq2zl9cy6dfdya"))))
-    (native-inputs
-     `(("unzip" ,unzip)))
+      (origin
+        (method url-fetch)
+        (uri (string-append
+              "http://effbot.org/downloads/Imaging-"
+              version ".tar.gz"))
+        (sha256
+          (base32
+            "141zidl3s9v4vfi3nsbg42iq1lc2a932gprqr1kij5hrnn53bmvx"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Adapt to newer freetype. As the package is unmaintained upstream,
+        ;; there is no use in creating a patch and reporting it.
+        '(substitute* "_imagingft.c"
+           (("freetype/")
+            "freetype2/")))))
+    (build-system python-build-system)
+    (inputs
+      `(("freetype" ,freetype)
+        ("libjpeg" ,libjpeg)
+        ("libtiff" ,libtiff)
+        ("python-setuptools" ,python-setuptools)
+        ("zlib" ,zlib)))
+    (arguments
+     ;; Only the fork python-pillow works with Python 3.
+     `(#:python ,python-2
+       #:tests? #f ; no check target
+       #:phases
+         (alist-cons-before
+          'build 'configure
+          ;; According to README and setup.py, manual configuration is
+          ;; the preferred way of "searching" for inputs.
+          ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter.
+          (lambda* (#:key inputs #:allow-other-keys)
+            (let ((jpeg (assoc-ref inputs "libjpeg"))
+                  (zlib (assoc-ref inputs "zlib"))
+                  (tiff (assoc-ref inputs "libtiff"))
+                  (freetype (assoc-ref inputs "freetype")))
+              (substitute* "setup.py"
+                (("JPEG_ROOT = None")
+                 (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")"))
+                (("ZLIB_ROOT = None")
+                 (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")"))
+                (("TIFF_ROOT = None")
+                 (string-append "TIFF_ROOT = libinclude(\"" tiff "\")"))
+                (("FREETYPE_ROOT = None")
+                 (string-append "FREETYPE_ROOT = libinclude(\""
+                                freetype "\")")))))
+          %standard-phases)))
+    (home-page "http://www.pythonware.com/products/pil/")
+    (synopsis "Python Imaging Library")
+    (description "The Python Imaging Library (PIL) adds image processing
+capabilities to the Python interpreter.")
+    (license (license:x11-style
+               "file://README"
+               "See 'README' in the distribution."))))
+
+(define-public python2-piddle-gn
+  (package
+    (name "python2-piddle")
+    (version "1.0.15-gn")
+    (source (origin
+     (method url-fetch)
+     (uri (string-append
+           "http://files.genenetwork.org/software/contrib/piddle-"
+version "-gn.tgz"))
+     (sha256
+      (base32
+       "0yl6frmhy94cmwzdks7ndc7nzh1ml2a4ch86gz2l7wcwpxjhwgmk"))))
 
     (build-system python-build-system)
     ;; (native-inputs
-- 
cgit v1.2.3


From 0660647c4bf43114a087337fa11131313afc7b9a Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 25 Feb 2016 09:29:13 +0000
Subject: Small GN database

---
 gn/packages/genenetwork.scm | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 2f755a6..dea6eae 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -178,7 +178,7 @@
               ("python2-pandas" ,python2-pandas)
               ("python2-parallel" ,python2-parallel)
               ("python2-passlib" ,python2-passlib)
-              ("python2-piddle" ,python2-piddle)
+              ("python2-piddle-gn2" ,python2-piddle-gn2)
               ("python2-redis" ,python2-redis)
               ("python2-requests" ,python2-requests)
               ("python2-rpy2" ,python2-rpy2)
@@ -202,3 +202,35 @@
 
 ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
 ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
+
+(define-public genenetwork2-database-small
+  (let ((md5 "93e745e9c"))
+    (package
+    (name "genenetwork2-database-small")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip")
+       (file-name (string-append name "-" md5)) 
+       (sha256
+        (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x"))))
+    (build-system trivial-build-system)
+    (native-inputs `(("unzip" ,unzip)
+                     ("source" ,source)))
+
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder (begin
+                   (use-modules (guix build utils))
+                   (let ((source (assoc-ref %build-inputs "source"))
+                         (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))
+                         )
+                   (and (mkdir "db")
+                        (zero? (system* unzip source "-d" "db"))
+                        (chdir "db"))))))
+    (home-page "http://genenetwork.org/")
+    (synopsis "Small database to run on genenetwork")
+    (description "Genenetwork installation + database.")
+    (license license:agpl3+))))
+
-- 
cgit v1.2.3


From 8c2f2f7f65441a3b66bc2d9b145cd9065461d0cc Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 25 Feb 2016 11:02:28 +0000
Subject: Fix python-piddle

---
 gn/packages/genenetwork.scm |  2 +-
 gn/packages/python.scm      | 17 +++++++++--------
 2 files changed, 10 insertions(+), 9 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index dea6eae..b77ccb4 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -178,7 +178,7 @@
               ("python2-pandas" ,python2-pandas)
               ("python2-parallel" ,python2-parallel)
               ("python2-passlib" ,python2-passlib)
-              ("python2-piddle-gn2" ,python2-piddle-gn2)
+              ("python2-piddle-gn" ,python2-piddle-gn)
               ("python2-redis" ,python2-redis)
               ("python2-requests" ,python2-requests)
               ("python2-rpy2" ,python2-rpy2)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 61d186b..7781521 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -426,19 +426,20 @@ capabilities to the Python interpreter.")
      (method url-fetch)
      (uri (string-append
            "http://files.genenetwork.org/software/contrib/piddle-"
-version "-gn.tgz"))
+version ".tgz"))
      (sha256
       (base32
-       "0yl6frmhy94cmwzdks7ndc7nzh1ml2a4ch86gz2l7wcwpxjhwgmk"))))
+       "05gjnn31v7p0kh58qixrpcizcxqf3b7zv4a5kk8nsmqwgxh0c6gq"))))
 
     (build-system python-build-system)
-    ;; (native-inputs
-    ;; `(("python-setuptools" ,python-setuptools)))
+    (native-inputs
+     `(("python2-setuptools" ,python2-setuptools)))
     (arguments
-     `(#:python ,python-2
-       #:tests? #f
-       ))   ; no 'setup.py test' really!
-    (home-page "http://www.numpy.org/")
+     `(
+       #:python ,python-2
+       #:tests? #f   ; no 'setup.py test' really!
+    ))
+    (home-page #f)
     (synopsis "Canvas drawing library for python2 (old!)")
     (description #f)
     (license #f)))
-- 
cgit v1.2.3


From 61435b2d111793806f19793655a3a187aec9562e Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Fri, 26 Feb 2016 08:43:13 +0000
Subject: Fix ruby error

---
 gn/packages/ruby.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm
index 0e1fa88..bebc678 100644
--- a/gn/packages/ruby.scm
+++ b/gn/packages/ruby.scm
@@ -16,7 +16,7 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
-(define-module (gnu packages ruby)
+(define-module (gn packages ruby)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
-- 
cgit v1.2.3


From b7db2ef030ce2c0845c172f8da27954f5c7a4fbf Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 10:41:19 +0000
Subject: Restarted r-wgcna

---
 gn/packages/bioinformatics.scm | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index bf39935..7b96604 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -61,23 +61,24 @@
           "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))
   (properties `((upstream-name . "WGCNA")))
   (build-system r-build-system)
-  ;; (propagated-inputs
-    ;; `( ;; ("r-annotationdbi" ,r-annotationdbi)
-       ;; ("r-doparallel" ,r-doparallel)
-       ;; ("r-dynamictreecut" ,r-dynamictreecut)
-       ;; ("r-fastcluster" ,r-fastcluster)
-       ;; ("r-foreach" ,r-foreach)
-       ;; ("r-go.db" ,r-go.db)
-       ;; ("r-grdevices" ,r-grdevices)
-       ;; ("r-hmisc" ,r-hmisc)
-       ;; ("r-impute" ,r-impute)
-       ;; ("r-matrixstats" ,r-matrixstats)
-       ;; ("r-parallel" ,r-parallel)
-       ;; ("r-preprocesscore" ,r-preprocesscore)
-       ;; ("r-splines" ,r-splines)
-       ;; ("r-stats" ,r-stats)
-       ;; ("r-survival" ,r-survival)
-       ;; ("r-utils" ,r-utils)))
+  (propagated-inputs
+   `( ;; ("r-annotationdbi" ,r-annotationdbi)
+     ("r-biocparallel" ,r-biocparallel)
+     ; ("r-dynamictreecut" ,r-dynamictreecut)
+     ; ("r-fastcluster" ,r-fastcluster)
+     ; ("r-foreach" ,r-foreach)
+     ("r-go-db" ,r-go-db)
+     ; ("r-grdevices" ,r-grdevices)
+     ; ("r-hmisc" ,r-hmisc)
+     ("r-impute" ,r-impute)
+     ("r-matrixstats" ,r-matrixstats)
+     ; ("r-parallel" ,r-parallel)
+     ; ("r-preprocesscore" ,r-preprocesscore)
+     ; ("r-splines" ,r-splines)
+     ; ("r-stats" ,r-stats)
+     ; ("r-survival" ,r-survival)
+     ; ("r-utils" ,r-utils)
+     ))
   (home-page
     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
   (synopsis
-- 
cgit v1.2.3


From 182c7797cc905faa1a2d497397ef465bbf484ca2 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 10:41:49 +0000
Subject: rdmd has moved into guix proper

---
 gn/packages/bioinformatics.scm | 42 ------------------------------------------
 1 file changed, 42 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 7b96604..405e5b3 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -269,48 +269,6 @@ mixed model and some of its close relatives for genome-wide
 association studies (GWAS).")
     (license license:gpl3))))
 
-(define-public rdmd
-  (let ((commit "4dba6877c"))
-    (package
-      (name "rdmd")
-      (version "20160217")
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/D-Programming-Language/tools.git")
-                      (commit commit)))
-                (file-name (string-append name "-" commit))
-                (sha256
-                 (base32
-                  "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
-      (build-system gnu-build-system)
-      (arguments
-       '(#:phases
-         (modify-phases %standard-phases
-           (delete 'configure)
-           (delete 'check) ; There is no Makefile, so there's no 'make check'.
-           (replace
-            'build
-            (lambda _
-              (zero? (system* "ldc2" "rdmd.d"))))
-           (replace
-            'install
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                (mkdir-p bin)
-                (copy-file "rdmd" (string-append bin "/rdmd"))))))))
-      (native-inputs
-       `(("ldc" ,ldc)))
-      (home-page "https://github.com/D-Programming-Language/tools/")
-      (synopsis "Tool for the D language which is used for compiling")
-      (description
-       "rdmd is a companion to the dmd compiler that simplifies the typical
-edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle.  Like
-make and other tools, rdmd uses the relative dates of the files involved to
-minimize the amount of work necessary.  Unlike make, rdmd tracks dependencies
-and freshness without requiring additional information from the user.")
-      (license license:boost1.0))))
-
 (define-public sambamba
   (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
     (package
-- 
cgit v1.2.3


From 42d110f144f36f6b1bf2092254ca3286094bb206 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 11:18:38 +0000
Subject: r-wgca: git fetch

---
 gn/packages/bioinformatics.scm | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 405e5b3..2bdf47a 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -49,25 +49,28 @@
   #:use-module (srfi srfi-1))
 
 (define-public r-wgcna
+  (let ((commit "9c68667c3"))
 (package
   (name "r-wgcna")
-  (version "1.48")
-  (source
-    (origin
-      (method url-fetch)
-      (uri (cran-uri "WGCNA" version))
-      (sha256
-        (base32
-          "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))
+  (version (string-append "1.49-" commit))
+  (source (origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/genenetwork/WGCNA.git")
+                 (commit commit)))
+           (file-name (string-append name "-" commit))
+           (sha256
+            (base32
+             "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf581"))))
   (properties `((upstream-name . "WGCNA")))
   (build-system r-build-system)
   (propagated-inputs
    `( ;; ("r-annotationdbi" ,r-annotationdbi)
-     ("r-biocparallel" ,r-biocparallel)
+     ; ("r-biocparallel" ,r-biocparallel)
      ; ("r-dynamictreecut" ,r-dynamictreecut)
      ; ("r-fastcluster" ,r-fastcluster)
      ; ("r-foreach" ,r-foreach)
-     ("r-go-db" ,r-go-db)
+     ; ("r-go-db" ,r-go-db)
      ; ("r-grdevices" ,r-grdevices)
      ; ("r-hmisc" ,r-hmisc)
      ("r-impute" ,r-impute)
@@ -85,7 +88,7 @@
     "Weighted Correlation Network Analysis")
   (description
     "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data.  Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits.  Also includes a number of utility functions for data manipulation and visualization.")
-  (license license:gpl2+)))
+  (license license:gpl2+))))
 
 (define-public qtlreaper
   (package
-- 
cgit v1.2.3


From d5a9e7dd0616461ec9960b9e57665dcc766d9b33 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 11:48:50 +0000
Subject: r-wgcna deps

---
 gn/packages/bioinformatics.scm | 24 +++++++-----
 gn/packages/statistics.scm     | 85 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 100 insertions(+), 9 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 2bdf47a..dd7e77e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -49,27 +49,28 @@
   #:use-module (srfi srfi-1))
 
 (define-public r-wgcna
-  (let ((commit "9c68667c3"))
+  (let ((commit "41b24edb522a200b671e8e25f6ffb67769113a49"))
 (package
   (name "r-wgcna")
   (version (string-append "1.49-" commit))
   (source (origin
            (method git-fetch)
            (uri (git-reference
-                 (url "https://github.com/genenetwork/WGCNA.git")
+                 ;; (url "https://github.com/genenetwork/WGCNA.git")
+                 (url "https://github.com/pjotrp/WGCNA.git")
                  (commit commit)))
            (file-name (string-append name "-" commit))
            (sha256
             (base32
-             "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf581"))))
+             "1ad2lgdz8dy8imn4my83jz4xqp4m3phyakfssmdjcp362g739p2w"))))
   (properties `((upstream-name . "WGCNA")))
   (build-system r-build-system)
   (propagated-inputs
    `( ;; ("r-annotationdbi" ,r-annotationdbi)
      ; ("r-biocparallel" ,r-biocparallel)
-     ; ("r-dynamictreecut" ,r-dynamictreecut)
-     ; ("r-fastcluster" ,r-fastcluster)
-     ; ("r-foreach" ,r-foreach)
+     ("r-dynamictreecut" ,r-dynamictreecut)
+     ("r-fastcluster" ,r-fastcluster)
+     ("r-foreach" ,r-foreach)
      ; ("r-go-db" ,r-go-db)
      ; ("r-grdevices" ,r-grdevices)
      ; ("r-hmisc" ,r-hmisc)
@@ -85,9 +86,14 @@
   (home-page
     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
   (synopsis
-    "Weighted Correlation Network Analysis")
+    "Weighted gene correlation network analysis (wgcna)")
   (description
-    "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data.  Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits.  Also includes a number of utility functions for data manipulation and visualization.")
+    "Functions necessary to perform Weighted Correlation Network
+Analysis on high-dimensional data.  Includes functions for rudimentary
+data cleaning, construction of correlation networks, module
+identification, summarization, and relating of variables and modules
+to sample traits.  Also includes a number of utility functions for
+data manipulation and visualization.")
   (license license:gpl2+))))
 
 (define-public qtlreaper
@@ -123,7 +129,7 @@ test.  For the permutation test, it performs only as many permutations
 as are necessary to define the empirical P-value to a reasonable
 precision. It also performs bootstrap resampling to estimate the
 confidence region for the location of a putative QTL.")
-    (license license:gpl2)))
+    (license license:gpl2+)))
 
 (define-public plink2
   (package
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 2d83816..57ddfe6 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -39,6 +39,91 @@
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-1))
 
+(define-public r-iterators
+(package
+  (name "r-iterators")
+  (version "1.0.8")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "iterators" version))
+      (sha256
+        (base32
+          "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
+  (build-system r-build-system)
+  ;; (propagated-inputs `(("r-utils" ,r-utils)))
+  (home-page
+    "http://cran.r-project.org/web/packages/iterators")
+  (synopsis "Provides Iterator Construct for R")
+  (description
+    "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.")
+  (license #f)))
+
+(define-public r-foreach
+(package
+  (name "r-foreach")
+  (version "1.4.3")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "foreach" version))
+      (sha256
+        (base32
+          "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
+  (build-system r-build-system)
+  (propagated-inputs `(("r-iterators" ,r-iterators)))
+  (home-page
+    "http://cran.r-project.org/web/packages/foreach")
+  (synopsis
+    "Provides Foreach Looping Construct for R")
+  (description
+    "Support for the foreach looping construct.  Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter.  This package in particular is intended to be used for its return value, rather than for its side effects.  In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function.  Using foreach without side effects also facilitates executing the loop in parallel.")
+  (license #f))
+)
+
+(define-public r-fastcluster
+(package
+  (name "r-fastcluster")
+  (version "1.1.16")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "fastcluster" version))
+      (sha256
+        (base32
+          "0x2prrsnqi5iqx23ki6y2agndjq8058ph6s703i4avrqi1q1w1q8"))))
+  (build-system r-build-system)
+  (home-page
+    "http://danifold.net/fastcluster.html")
+  (synopsis
+    "Fast Hierarchical Clustering Routines for R and Python")
+  (description
+    "This is a two-in-one package which provides interfaces to both R and Python.  It implements fast hierarchical, agglomerative clustering routines.  Part of the functionality is designed as drop-in replacement for existing routines: \"linkage\" in the SciPy package \"scipy.cluster.hierarchy\", \"hclust\" in R's \"stats\" package, and the \"flashClust\" package.  It provides the same functionality with the benefit of a much faster implementation.  Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide.  For information on how to install the Python files, see the file INSTALL in the source distribution.")
+  (license #f)))
+
+(define-public r-dynamictreecut
+(package
+  (name "r-dynamictreecut")
+  (version "1.62")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "dynamicTreeCut" version))
+      (sha256
+        (base32
+          "1y11gg6k32wpsyb10kdv176ivczx2jlizs1xsrjrs6iwbncwzrkp"))))
+  (properties
+    `((upstream-name . "dynamicTreeCut")))
+  (build-system r-build-system)
+  ; (propagated-inputs `(("r-stats" ,r-stats)))
+  (home-page
+    "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
+  (synopsis
+    "Methods for detection of clusters in hierarchical clustering dendrograms.")
+  (description
+    "Contains methods for detection of clusters in hierarchical clustering dendrograms.")
+  (license license:gpl2+)))
+
 (define-public r-rcppeigen
 (package
   (name "r-rcppeigen")
-- 
cgit v1.2.3


From 71684ab0577b60b53d4a459e97bb5540952ea4d9 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 12:45:40 +0000
Subject: r-wgcna deps

---
 gn/packages/bioinformatics.scm | 12 ++++--
 gn/packages/statistics.scm     | 85 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+), 4 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index dd7e77e..92be2b4 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -49,7 +49,7 @@
   #:use-module (srfi srfi-1))
 
 (define-public r-wgcna
-  (let ((commit "41b24edb522a200b671e8e25f6ffb67769113a49"))
+  (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb"))
 (package
   (name "r-wgcna")
   (version (string-append "1.49-" commit))
@@ -62,18 +62,19 @@
            (file-name (string-append name "-" commit))
            (sha256
             (base32
-             "1ad2lgdz8dy8imn4my83jz4xqp4m3phyakfssmdjcp362g739p2w"))))
+             "1zqnsb8s3065rq1y2y3l79zi8wmdwjkcjls96ypycrb7pmdil58j"))))
   (properties `((upstream-name . "WGCNA")))
   (build-system r-build-system)
   (propagated-inputs
    `( ;; ("r-annotationdbi" ,r-annotationdbi)
      ; ("r-biocparallel" ,r-biocparallel)
      ("r-dynamictreecut" ,r-dynamictreecut)
+     ("r-doparallel" ,r-doparallel)
      ("r-fastcluster" ,r-fastcluster)
      ("r-foreach" ,r-foreach)
-     ; ("r-go-db" ,r-go-db)
+     ("r-go-db" ,r-go-db)
      ; ("r-grdevices" ,r-grdevices)
-     ; ("r-hmisc" ,r-hmisc)
+     ("r-hmisc" ,r-hmisc)
      ("r-impute" ,r-impute)
      ("r-matrixstats" ,r-matrixstats)
      ; ("r-parallel" ,r-parallel)
@@ -83,6 +84,9 @@
      ; ("r-survival" ,r-survival)
      ; ("r-utils" ,r-utils)
      ))
+    (arguments
+     `(
+       #:tests? #f))   ; no 'setup.py test'
   (home-page
     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
   (synopsis
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 57ddfe6..cc2726c 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -18,6 +18,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages file)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages machine-learning)
@@ -39,6 +40,90 @@
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-1))
 
+(define-public r-acepack
+(package
+  (name "r-acepack")
+  (version "1.3-3.3")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "acepack" version))
+      (sha256
+        (base32
+          "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y"))))
+  (build-system r-build-system)
+  (inputs
+   `(("gfortran" ,gfortran)))
+  (home-page
+    "http://cran.r-project.org/web/packages/acepack")
+  (synopsis
+    "ace() and avas() for selecting regression transformations")
+  (description
+    "ACE and AVAS methods for choosing regression transformations.")
+  (license license:x11)))
+
+(define-public r-hmisc
+(package
+  (name "r-hmisc")
+  (version "3.17-2")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "Hmisc" version))
+      (sha256
+        (base32
+          "110w5hbrl10isslqs0iq6w2ll0dafqyqznb50cdcallnlnvbvxrg"))))
+  (properties `((upstream-name . "Hmisc")))
+  (build-system r-build-system)
+  (propagated-inputs
+    `(("r-acepack" ,r-acepack)
+      ; ("r-cluster" ,r-cluster)
+      ; ("r-foreign" ,r-foreign)
+      ; ("r-formula" ,r-formula)
+      ("r-ggplot2" ,r-ggplot2)
+      ; ("r-grid" ,r-grid)
+      ("r-gridextra" ,r-gridextra)
+      ("r-gtable" ,r-gtable)
+      ("r-lattice" ,r-lattice)
+      ; ("r-latticeextra" ,r-latticeextra)
+      ; ("r-methods" ,r-methods)
+      ; ("r-nnet" ,r-nnet)
+      ; ("r-rpart" ,r-rpart)
+                                        ; ("r-survival" ,r-survival)))
+      ))
+  (home-page
+    "http://biostat.mc.vanderbilt.edu/Hmisc")
+  (synopsis "Harrell Miscellaneous")
+  (description
+    "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.")
+  (license license:gpl2+)))
+
+(define-public r-doparallel
+(package
+  (name "r-doparallel")
+  (version "1.0.10")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "doParallel" version))
+      (sha256
+        (base32
+          "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
+  (properties `((upstream-name . "doParallel")))
+  (build-system r-build-system)
+  (propagated-inputs
+    `(("r-foreach" ,r-foreach)
+      ("r-iterators" ,r-iterators)
+      ;; ("r-parallel" ,r-parallel)
+      ))
+  (home-page
+    "http://cran.r-project.org/web/packages/doParallel")
+  (synopsis
+    "Foreach Parallel Adaptor for the 'parallel' Package")
+  (description
+    "Provides a parallel backend for the %dopar% function using the parallel package.")
+  (license license:gpl2+)))
+
 (define-public r-iterators
 (package
   (name "r-iterators")
-- 
cgit v1.2.3


From b280af1638843cc3b3ca14933a07b66076b0713d Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 13:03:03 +0000
Subject: r-wgcna deps

---
 gn/packages/statistics.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 54 insertions(+), 2 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index cc2726c..2c9ebda 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -62,6 +62,54 @@
     "ACE and AVAS methods for choosing regression transformations.")
   (license license:x11)))
 
+(define-public r-latticeextra
+(package
+  (name "r-latticeextra")
+  (version "0.6-28")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "latticeExtra" version))
+      (sha256
+        (base32
+          "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
+  (properties `((upstream-name . "latticeExtra")))
+  (build-system r-build-system)
+  (propagated-inputs
+    `( ;;("r-grdevices" ,r-grdevices)
+      ("r-gridbase" ,r-gridbase)
+      ("r-lattice" ,r-lattice)
+      ("r-rcolorbrewer" ,r-rcolorbrewer)
+      ))
+  (home-page
+    "http://latticeextra.r-forge.r-project.org/")
+  (synopsis
+    "Extra Graphical Utilities Based on Lattice")
+  (description
+    "Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.")
+  (license license:gpl2+)))
+
+(define-public r-formula
+  (package
+  (name "r-formula")
+  (version "1.2-1")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "Formula" version))
+      (sha256
+        (base32
+          "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax"))))
+  (properties `((upstream-name . "Formula")))
+  (build-system r-build-system)
+  (home-page
+    "http://cran.r-project.org/web/packages/Formula")
+  (synopsis "Extended Model Formulas")
+  (description
+    "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.")
+  (license #f))
+)
+
 (define-public r-hmisc
 (package
   (name "r-hmisc")
@@ -75,17 +123,21 @@
           "110w5hbrl10isslqs0iq6w2ll0dafqyqznb50cdcallnlnvbvxrg"))))
   (properties `((upstream-name . "Hmisc")))
   (build-system r-build-system)
+  (inputs
+   `(("gfortran" ,gfortran)))
+  (arguments
+   `(#:tests? #f))   ; no 'setup.py test'
   (propagated-inputs
     `(("r-acepack" ,r-acepack)
       ; ("r-cluster" ,r-cluster)
       ; ("r-foreign" ,r-foreign)
-      ; ("r-formula" ,r-formula)
+      ("r-formula" ,r-formula)
       ("r-ggplot2" ,r-ggplot2)
       ; ("r-grid" ,r-grid)
       ("r-gridextra" ,r-gridextra)
       ("r-gtable" ,r-gtable)
       ("r-lattice" ,r-lattice)
-      ; ("r-latticeextra" ,r-latticeextra)
+      ("r-latticeextra" ,r-latticeextra)
       ; ("r-methods" ,r-methods)
       ; ("r-nnet" ,r-nnet)
       ; ("r-rpart" ,r-rpart)
-- 
cgit v1.2.3


From f82b7c5b7ef5bdb9761e48761f683d62d3a05c48 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 28 Feb 2016 17:42:06 +0000
Subject: r-wgcna deps

---
 gn/packages/bioinformatics.scm | 24 +++++++++++++++++++++++-
 gn/packages/genenetwork.scm    |  1 +
 2 files changed, 24 insertions(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 92be2b4..b503e22 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -48,6 +48,28 @@
   #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
+
+(define-public r-biocpreprocesscore
+  (package
+    (name "r-biocpreprocesscore")
+    (version "1.32.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "preprocessCore" version))
+              (sha256
+               (base32
+                "07isghjkqm91rg37l1fzpjrbq36b7w4pbsi95wwh6a8qq7r69z1n"))))
+    (properties
+     `((upstream-name . "BiocpreprocessCore")
+       (r-repository . bioconductor)))
+    (build-system r-build-system)
+    (home-page "http://bioconductor.org/packages/preprocessCore")
+    (synopsis "Preprocess functions for Bioconductor")
+    (description
+     "A library of core preprocessing routines.")
+    (license license:lgpl2.0+)))
+
+
 (define-public r-wgcna
   (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb"))
 (package
@@ -78,7 +100,7 @@
      ("r-impute" ,r-impute)
      ("r-matrixstats" ,r-matrixstats)
      ; ("r-parallel" ,r-parallel)
-     ; ("r-preprocesscore" ,r-preprocesscore)
+     ("r-biocpreprocesscore" ,r-biocpreprocesscore)
      ; ("r-splines" ,r-splines)
      ; ("r-stats" ,r-stats)
      ; ("r-survival" ,r-survival)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index b77ccb4..033bf94 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -158,6 +158,7 @@
     (propagated-inputs `(  ;; propagated for development purposes
               ("python" ,python-2) ;; probably superfluous
               ("r" ,r)
+              ("r-wgcna" ,r-wgcna)
               ("redis" ,redis)
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
-- 
cgit v1.2.3