From dd74ba8cd335ac94dca916549a2b9edbc0332748 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 20 Feb 2016 13:07:43 +0000
Subject: Adding pylmm to gn2

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

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1aee0ef..0d3a765 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -44,6 +44,7 @@
   #:use-module (gnu packages zip)
   #:use-module (gnu packages bootstrap)
   #:use-module (gn packages python)
+  #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
 (define-public my-deploy
@@ -380,6 +381,7 @@ association studies (GWAS).")
     (inputs `(
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
+              ("pylmm-gn2" ,pylmm-gn2)
               ("plink2" ,plink-ng)
               ("nginx" ,nginx)
               ("python2-flask" ,python2-flask)
-- 
cgit v1.2.3


From 1574a0e0478e921905a2fad4ff3ff0f2c196b6f1 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 21 Feb 2016 08:01:25 +0000
Subject: Removed non-compiling packages

---
 gn/packages/bioinformatics.scm | 51 +-----------------------------------------
 1 file changed, 1 insertion(+), 50 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 75b9de7..af5cfba 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -26,6 +26,7 @@
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages ldc)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages ncurses)
@@ -34,7 +35,6 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages ruby)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tbb)
   #:use-module (gnu packages textutils)
@@ -492,52 +492,3 @@ subset of samtools functionality, including view, index, sort,
 markdup, and depth.")
     (license license:gpl2+)))
 
-(define-public picard
-  (package
-    (name "picard")
-    (version "2.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/broadinstitute/picard/archive/"
-             version ".tar.gz"))
-       (sha256
-        (base32 ""))))
-    (home-page "http://broadinstitute.github.io/picard/")
-    (synopsis "A set of Java command line tools for manipulating high-throughput
-sequencing data (HTS) data and formats")
-    (description "Picard comprises Java-based command-line utilities that
-manipulate SAM files, and a Java API (HTSJDK) for creating new programs that
-read and write SAM files. Both SAM text format and SAM binary (BAM) format are
-supported.")
-    ;; The license is MIT.
-    (license license:expat)
-))
-
-(define-public fastqc
-  (package
-    (name "fastqc")
-    (version "0.11.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"
-             version "_source.zip"))
-       (sha256
-        (base32 ""))))
-    (build-system gnu-build-system)
-    (arguments
-     `(("perl" ,perl) ; Needed to run the java command.
-       ("jdk" ,icedtea "jdk")))
-    (native-inputs
-     `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK..
-       ("jdk" ,icedtea "jdk")
-       ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy.
-       ("unzip" ,unzip)))
-    (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
-    (synopsis "A quality control tool for high throughput sequence data")
-    (description
-     "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.")
-    (license license:gpl3+)))
-- 
cgit v1.2.3


From 2933faad1298777e76584fff3b6fc0bcaa6c50b1 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 21 Feb 2016 11:32:31 +0000
Subject: * gn/bioinformatics.scm: Sambamba using git checkout and compiles
 with Makefile.guix

---
 gn/packages/bioinformatics.scm | 32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1d65b4c..896767b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,7 +10,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
-  #:use-module (guix build-system ruby)
+  ;; #:use-module (guix build-system ruby)
   #:use-module (guix build-system r)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -459,17 +459,20 @@ internally during various build tasks.")
     (license license:boost1.0)))
 
 (define-public sambamba
+  (let ((commit "2ca5a2dba"))
   (package
     (name "sambamba")
-    (version "0.5.9")
+    (version (string-append "0.5.9-" commit))
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/lomereiter/sambamba/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append "sambamba-" version ".tar.gz"))
-              (sha256
-               (base32 "152zbg4m10ikr7xgk20c0nwqwrqvydmpc73p2c1fqmbhpk0l0ws6"))))
+             (method git-fetch)
+             (uri (git-reference                
+                   ;; https://github.com/pjotrp/sambamba.git
+                   (url "https://github.com/pjotrp/sambamba.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
     (build-system gnu-build-system)
     (inputs
      `(("ldc" ,ldc)
@@ -512,16 +515,17 @@ internally during various build tasks.")
              ;; for Guix, this should be resolved on Sambamba upstream.  For
              ;; now, just extract the source code to the desired directory.
              (and (with-directory-excursion "htslib"
-                    (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
-                                    "--strip-components=1")))
-                  (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD")))))
+              (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
+                              "--strip-components=1")))
+              (zero? (system* "cp" "-R" (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.
          (replace
           'build
           (lambda* (#:key (make-flags '()) #:allow-other-keys)
-            (zero? (system* "make" "sambamba-ldmd2-64" make-flags)))))))
+            (zero? (system* "make" "-f" "Makefile.guix" make-flags)))))))
     (home-page "https://github.com/lomereiter/sambamba")
     (synopsis "A tool for working with SAM and BAM files written in D.")
     (description
@@ -530,7 +534,7 @@ library), written in the D programming language, for working with SAM
 and BAM files.  Current parallelised functionality is an important
 subset of samtools functionality, including view, index, sort,
 markdup, and depth.")
-    (license license:gpl2+)))
+    (license license:gpl2+))))
 
 (define-public picard
   (package
-- 
cgit v1.2.3


From 96706fd977738f6ca3eb981591ced6c7db833887 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Mon, 22 Feb 2016 08:50:37 +0000
Subject: Moving genenetwork stuff into its own module

---
 gn/packages/bioinformatics.scm | 151 -------------------------------
 gn/packages/genenetwork.scm    | 200 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 200 insertions(+), 151 deletions(-)
 create mode 100644 gn/packages/genenetwork.scm

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 896767b..43e61a2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -47,45 +47,6 @@
   #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
-(define-public my-deploy
-  (package
-    (name "my-deploy")
-    (version "0.0.1")
-    (source #f)
-    (build-system trivial-build-system)
-    (arguments
-     `(#:guile ,%bootstrap-guile
-       #:modules ((guix build utils))
-       #:builder
-       (let* ((out  (assoc-ref %outputs "out"))
-              (bash (assoc-ref %build-inputs "bash"))
-              (foo  (string-append out "/foo")))
-         (begin
-           (use-modules (guix build utils))
-           (mkdir out)
-           (call-with-output-file foo
-             (lambda (p)
-               (format p
-                       "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
-                       bash)))
-           (chmod foo #o777)
-           ;; wrap-program uses `which' to find bash for the wrapper
-           ;; shebang, but it can't know about the bootstrap bash in
-           ;; the store, since it's not named "bash".  Help it out a
-           ;; bit by providing a symlink it this package's output.
-           (symlink bash (string-append out "/bash"))
-           (setenv "PATH" out)
-           (wrap-program foo `("GUIX_FOO" prefix ("hello")))
-           (wrap-program foo `("GUIX_BAR" prefix ("world")))
-           #t))))
-    (inputs `(("bash" ,(search-bootstrap-binary "bash"
-                                                (%current-system)))))
-
-    (home-page #f)
-    (synopsis #f)
-    (description #f)
-    (license #f)))
-
 (define-public r-wgcna
 (package
   (name "r-wgcna")
@@ -307,118 +268,6 @@ association studies (GWAS).")
     (license license:gpl3))))
 
 
-(define-public genenetwork1
-  (let ((commit "d622c803b"))
-  (package
-    (name "genenetwork1")
-    (version (string-append "1.0-" commit ))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/genenetwork/genenetwork.git")
-                   ;; (url "https://github.com/pjotrp/genenetwork.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit)) 
-             (sha256
-              (base32
-               "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
-    (propagated-inputs `(
-              ("python" ,python-2) ;; probably superfluous
-              ("r" ,r) 
-    ))
-    (inputs `(
-              ;; http://spring211.uthsc.edu/gn/thirdparty.tbz
-              ;; graphviz-2.22.2  htmlgen  json  numarray-1.5.2  piddle  PIL  pp-1.5.7  pyx  pyXLWriter  svg
-              ("mysql" ,mysql)
-              ("nginx" ,nginx)
-              ("graphviz" ,graphviz)
-              ; ("python2-jinja2" ,python2-jinja2)
-              ; ("python2-sqlalchemy" ,python2-sqlalchemy)
-              ; ("python2-setuptools" ,python2-setuptools)
-              ; ("python2-scipy" ,python2-scipy)
-              ;; looks like python-numarray is not needed
-              ; ("python2-numpy" ,python2-numpy)
-              ; ("python2-pandas" ,python2-pandas)
-              ; ("python2-passlib" ,python2-passlib)
-              ; ("python2-redis" ,python2-redis)
-              ; ("python2-requests" ,python2-requests)
-              ; ("python2-simplejson" ,python2-simplejson)
-              ; ("python2-pyyaml" ,python2-pyyaml)
-              ;; python-yolk is not needed
-              ("python2-pil" ,python2-pil)
-              ("python2-numarray" ,python2-numarray)
-              ("plink" ,plink) ;; gn1
-              ; ("r-qtl" ,r-qtl)
-              ))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f))   ; no 'setup.py test'
-    (home-page "http://genenetwork.org/")
-    (synopsis "Full genenetwork services")
-    (description "Genenetwork installation sumo.")
-    (license license:agpl3+))))
-
-(define-public genenetwork2
-  (let ((commit "9e9475053"))
-  (package
-    (name "genenetwork2")
-    (version (string-append "2.0-" commit ))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
-                   (url "https://github.com/pjotrp/genenetwork2.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit)) 
-             (sha256
-              (base32
-               "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
-    (propagated-inputs `(  ;; propagated for development purposes
-              ("python" ,python-2) ;; probably superfluous
-              ("r" ,r)
-              ("redis" ,redis)
-              ("mysql" ,mysql)
-              ("gemma" ,gemma-git)
-              ("pylmm-gn2" ,pylmm-gn2)
-              ("plink2" ,plink-ng)
-              ("nginx" ,nginx)
-              ("python2-flask" ,python2-flask)
-              ("python2-htmlgen-gn" ,python2-htmlgen-gn)
-              ("python2-jinja2" ,python2-jinja2)
-              ("python2-sqlalchemy" ,python2-sqlalchemy)
-              ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
-              ("python2-setuptools" ,python2-setuptools)
-              ("python2-scipy" ,python2-scipy)
-              ;; looks like python-numarray is not needed
-              ("python2-mysqlclient" ,python2-mysqlclient)
-              ("python2-numarray" ,python2-numarray)
-              ("python2-numpy" ,python2-numpy)
-              ("python2-pandas" ,python2-pandas)
-              ("python2-parallel" ,python2-parallel)
-              ("python2-passlib" ,python2-passlib)
-              ("python2-piddle" ,python2-piddle)
-              ("python2-redis" ,python2-redis)
-              ("python2-requests" ,python2-requests)
-              ("python2-rpy2" ,python2-rpy2)
-              ("python2-scipy" ,python2-scipy)
-              ("python2-simplejson" ,python2-simplejson)
-              ("python2-pyyaml" ,python2-pyyaml)
-              ("python2-xlsxwriter" ,python2-xlsxwriter)
-              ;; python-yolk is not needed
-              ("plink" ,plink) 
-              ("qtlreaper" ,qtlreaper) 
-              ("r-qtl" ,r-qtl)
-              ))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f))   ; no 'setup.py test'
-    (home-page "http://genenetwork.org/")
-    (synopsis "Full genenetwork services")
-    (description "Genenetwork installation sumo.")
-    (license license:agpl3+))))
-
 (define-public rdmd
   (package
     (name "rdmd")
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
new file mode 100644
index 0000000..b2e7f00
--- /dev/null
+++ b/gn/packages/genenetwork.scm
@@ -0,0 +1,200 @@
+;; Bioinformatics module
+
+(define-module (gn packages genenetwork)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
+  ;; #:use-module (guix build-system ruby)
+  #:use-module (guix build-system r)
+  #:use-module (guix build-system trivial)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages cpio)
+  #:use-module (gnu packages file)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages ldc)
+  #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages protobuf)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages vim)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages zip)
+  #:use-module (gnu packages bootstrap)
+  #:use-module (gn packages python)
+  #:use-module (gn packages statistics)
+  #:use-module (srfi srfi-1))
+
+(define-public my-deploy
+  (package
+    (name "my-deploy")
+    (version "0.0.1")
+    (source #f)
+    (build-system trivial-build-system)
+    (arguments
+     `(#:guile ,%bootstrap-guile
+       #:modules ((guix build utils))
+       #:builder
+       (let* ((out  (assoc-ref %outputs "out"))
+              (bash (assoc-ref %build-inputs "bash"))
+              (foo  (string-append out "/foo")))
+         (begin
+           (use-modules (guix build utils))
+           (mkdir out)
+           (call-with-output-file foo
+             (lambda (p)
+               (format p
+                       "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
+                       bash)))
+           (chmod foo #o777)
+           ;; wrap-program uses `which' to find bash for the wrapper
+           ;; shebang, but it can't know about the bootstrap bash in
+           ;; the store, since it's not named "bash".  Help it out a
+           ;; bit by providing a symlink it this package's output.
+           (symlink bash (string-append out "/bash"))
+           (setenv "PATH" out)
+           (wrap-program foo `("GUIX_FOO" prefix ("hello")))
+           (wrap-program foo `("GUIX_BAR" prefix ("world")))
+           #t))))
+    (inputs `(("bash" ,(search-bootstrap-binary "bash"
+                                                (%current-system)))))
+
+    (home-page #f)
+    (synopsis #f)
+    (description #f)
+    (license #f)))
+
+
+(define-public genenetwork1
+  (let ((commit "d622c803b"))
+  (package
+    (name "genenetwork1")
+    (version (string-append "1.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/genenetwork/genenetwork.git")
+                   ;; (url "https://github.com/pjotrp/genenetwork.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
+    (propagated-inputs `(
+              ("python" ,python-2) ;; probably superfluous
+              ("r" ,r) 
+    ))
+    (inputs `(
+              ;; http://spring211.uthsc.edu/gn/thirdparty.tbz
+              ;; graphviz-2.22.2  htmlgen  json  numarray-1.5.2  piddle  PIL  pp-1.5.7  pyx  pyXLWriter  svg
+              ("mysql" ,mysql)
+              ("nginx" ,nginx)
+              ("graphviz" ,graphviz)
+              ; ("python2-jinja2" ,python2-jinja2)
+              ; ("python2-sqlalchemy" ,python2-sqlalchemy)
+              ; ("python2-setuptools" ,python2-setuptools)
+              ; ("python2-scipy" ,python2-scipy)
+              ;; looks like python-numarray is not needed
+              ; ("python2-numpy" ,python2-numpy)
+              ; ("python2-pandas" ,python2-pandas)
+              ; ("python2-passlib" ,python2-passlib)
+              ; ("python2-redis" ,python2-redis)
+              ; ("python2-requests" ,python2-requests)
+              ; ("python2-simplejson" ,python2-simplejson)
+              ; ("python2-pyyaml" ,python2-pyyaml)
+              ;; python-yolk is not needed
+              ("python2-pil" ,python2-pil)
+              ("python2-numarray" ,python2-numarray)
+              ("plink" ,plink) ;; gn1
+              ; ("r-qtl" ,r-qtl)
+              ))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test'
+    (home-page "http://genenetwork.org/")
+    (synopsis "Full genenetwork services")
+    (description "Genenetwork installation sumo.")
+    (license license:agpl3+))))
+
+(define-public genenetwork2
+  (let ((commit "9e9475053"))
+  (package
+    (name "genenetwork2")
+    (version (string-append "2.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
+                   (url "https://github.com/pjotrp/genenetwork2.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
+    (propagated-inputs `(  ;; propagated for development purposes
+              ("python" ,python-2) ;; probably superfluous
+              ("r" ,r)
+              ("redis" ,redis)
+              ("mysql" ,mysql)
+              ("gemma" ,gemma-git)
+              ("pylmm-gn2" ,pylmm-gn2)
+              ("plink2" ,plink-ng)
+              ("nginx" ,nginx)
+              ("python2-flask" ,python2-flask)
+              ("python2-htmlgen-gn" ,python2-htmlgen-gn)
+              ("python2-jinja2" ,python2-jinja2)
+              ("python2-sqlalchemy" ,python2-sqlalchemy)
+              ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
+              ("python2-setuptools" ,python2-setuptools)
+              ("python2-scipy" ,python2-scipy)
+              ;; looks like python-numarray is not needed
+              ("python2-mysqlclient" ,python2-mysqlclient)
+              ("python2-numarray" ,python2-numarray)
+              ("python2-numpy" ,python2-numpy)
+              ("python2-pandas" ,python2-pandas)
+              ("python2-parallel" ,python2-parallel)
+              ("python2-passlib" ,python2-passlib)
+              ("python2-piddle" ,python2-piddle)
+              ("python2-redis" ,python2-redis)
+              ("python2-requests" ,python2-requests)
+              ("python2-rpy2" ,python2-rpy2)
+              ("python2-scipy" ,python2-scipy)
+              ("python2-simplejson" ,python2-simplejson)
+              ("python2-pyyaml" ,python2-pyyaml)
+              ("python2-xlsxwriter" ,python2-xlsxwriter)
+              ;; python-yolk is not needed
+              ("plink" ,plink) 
+              ("qtlreaper" ,qtlreaper) 
+              ("r-qtl" ,r-qtl)
+              ))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test'
+    (home-page "http://genenetwork.org/")
+    (synopsis "Full genenetwork services")
+    (description "Genenetwork installation sumo.")
+    (license license:agpl3+))))
-- 
cgit v1.2.3


From 03ebb3b1a374406039494bdf5d0cb1493ddb97d8 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Mon, 22 Feb 2016 10:43:18 +0100
Subject: Made rdmd-specific package from the tools repository.

---
 gn/packages/bioinformatics.scm | 78 ++++++++++++++++++++++--------------------
 1 file changed, 41 insertions(+), 37 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index b7384ef..1b4680e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -418,43 +418,47 @@ association studies (GWAS).")
     (license license:agpl3+))))
 
 (define-public rdmd
-  (package
-    (name "rdmd")
-    (version "20160217")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/D-Programming-Language/tools.git")
-                    (commit "4dba6877c481c1a911a7d50714da8fbd80022f0e")))
-              (file-name (string-append name "-" version "-checkout"))
-              (sha256
-               (base32
-                "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
-    (build-system gnu-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (delete '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
-     `(("gcc" ,gcc)
-       ("ldc" ,ldc)))
-    (home-page "https://github.com/D-Programming-Language/tools/")
-    (synopsis "Extra tools for building D programs")
-    (description
-     "This repository hosts various tools redistributed with DMD or used
-internally during various build tasks.")
-    (license license:boost1.0)))
+  (let ((commit "4dba6877c481c1a911a7d50714da8fbd80022f0e"))
+    (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)
+           (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
+       `(("gcc" ,gcc)
+         ("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
   (package
-- 
cgit v1.2.3


From 10e42d4dd2590dc6625bff974d5086fb2bd9ee8a Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Mon, 22 Feb 2016 11:08:36 +0100
Subject: Further rdmd refinements.

---
 gn/packages/bioinformatics.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 80fe134..67096b0 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -267,9 +267,8 @@ mixed model and some of its close relatives for genome-wide
 association studies (GWAS).")
     (license license:gpl3))))
 
-
 (define-public rdmd
-  (let ((commit "4dba6877c481c1a911a7d50714da8fbd80022f0e"))
+  (let ((commit "4dba6877c"))
     (package
       (name "rdmd")
       (version "20160217")
@@ -287,10 +286,10 @@ association studies (GWAS).")
        '(#:phases
          (modify-phases %standard-phases
            (delete 'configure)
-           (delete 'check)
+           (delete 'check) ; There is no Makefile, so there's no 'make check'.
            (replace
             'build
-            (lambda* _
+            (lambda _
               (zero? (system* "ldc2" "rdmd.d"))))
            (replace
             'install
@@ -299,8 +298,7 @@ association studies (GWAS).")
                 (mkdir-p bin)
                 (copy-file "rdmd" (string-append bin "/rdmd"))))))))
       (native-inputs
-       `(("gcc" ,gcc)
-         ("ldc" ,ldc)))
+       `(("ldc" ,ldc)))
       (home-page "https://github.com/D-Programming-Language/tools/")
       (synopsis "Tool for the D language which is used for compiling")
       (description
-- 
cgit v1.2.3


From 9aea3e8744c11a2f108165260aa8a59a1f346cdc Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Mon, 22 Feb 2016 11:17:08 +0100
Subject: Made it 'guix lint'-proof.

---
 gn/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 67096b0..098411e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -277,7 +277,7 @@ association studies (GWAS).")
                 (uri (git-reference
                       (url "https://github.com/D-Programming-Language/tools.git")
                       (commit commit)))
-                (file-name (string-append name "-" commit)) 
+                (file-name (string-append name "-" commit))
                 (sha256
                  (base32
                   "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
@@ -303,9 +303,9 @@ association studies (GWAS).")
       (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
+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
+minimize the amount of work necessary.  Unlike make, rdmd tracks dependencies
 and freshness without requiring additional information from the user.")
       (license license:boost1.0))))
 
-- 
cgit v1.2.3


From 6c2c0499e817badf1cc41822dfdf813e065a34a3 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Tue, 23 Feb 2016 10:38:55 +0100
Subject: Using my own fork of the Sambamba repository.

---
 gn/packages/bioinformatics.scm | 155 ++++++++++++++++++++++-------------------
 1 file changed, 85 insertions(+), 70 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 098411e..cfc5dae 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -310,82 +310,97 @@ and freshness without requiring additional information from the user.")
       (license license:boost1.0))))
 
 (define-public sambamba
-  (let ((commit "2ca5a2dba"))
-  (package
-    (name "sambamba")
-    (version (string-append "0.5.9-" commit))
-    (source (origin
+  (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
+  ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+    (package
+      (name "sambamba")
+      (version (string-append "0.5.9-" commit))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference                
+              ;; https://github.com/pjotrp/sambamba.git
+              (url "https://github.com/roelj/sambamba.git")
+              (commit commit)))
+        (file-name (string-append name "-" (string-take commit 7)))
+        (sha256
+         (base32
+          ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
+          "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"))))
+      (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)
+         ("gcc" ,gcc)
+         ("lz4-src"
+          ,(origin
+             (method url-fetch)
+             (uri (string-append
+                   "https://github.com/Cyan4973/lz4/archive/r131.tar.gz"))
+             (file-name "lz4-131.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 (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
+         ("biod-src"
+          ,(origin
              (method git-fetch)
-             (uri (git-reference                
-                   ;; https://github.com/pjotrp/sambamba.git
-                   (url "https://github.com/pjotrp/sambamba.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit)) 
+             (uri (git-reference
+                   (url "https://github.com/biod/BioD.git")
+                   (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
              (sha256
-              (base32
-               "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)
-       ("gcc" ,gcc)
-       ("rdmd" ,rdmd)
-       ("htslib-src"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append
-                 "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
-           (file-name (string-append "htslib-0.2.0-rc10.tar.gz"))
-           (sha256
-            (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
-       ("biod-src"
-        ,(origin
-           (method git-fetch)
-           (uri (git-reference
-                 (url "https://github.com/biod/BioD.git")
-                 (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
-           (sha256
-            (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
-           (file-name "biod")))))
-    (arguments
-     '(#:phases 
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (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.
-             (and (with-directory-excursion "htslib"
-              (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
-                              "--strip-components=1")))
-              (zero? (system* "cp" "-R" (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.
-         (replace
-          'build
-          (lambda* (#:key (make-flags '()) #:allow-other-keys)
-            (zero? (system* "make" "-f" "Makefile.guix" make-flags)))))))
-    (home-page "https://github.com/lomereiter/sambamba")
-    (synopsis "A tool for working with SAM and BAM files written in D.")
-    (description
-     "Sambamba is a high performance modern robust and fast tool (and
+              (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
+             (file-name "biod-src")))))
+      (arguments
+       `(#:tests? #f
+         #:make-flags (list "CC=gcc" "D_COMPILER=ldc2")
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (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.
+               (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")))
+                    (zero? (system* "ln" "--symbolic" (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.
+           (replace
+            'build
+            (lambda* (#:key inputs #:allow-other-keys)
+              (zero? (system* "make" "sambamba-ldmd2-64")))))))
+      (home-page "https://github.com/lomereiter/sambamba")
+      (synopsis "A tool for working with SAM and BAM files written in D.")
+      (description
+       "Sambamba is a high performance modern robust and fast tool (and
 library), written in the D programming language, for working with SAM
 and BAM files.  Current parallelised functionality is an important
 subset of samtools functionality, including view, index, sort,
 markdup, and depth.")
-    (license license:gpl2+))))
+      (license license:gpl2+))))
 
 (define-public picard
   (package
-- 
cgit v1.2.3


From 609d1a24c9700b8de72ddba4d5b8f091e4bd0828 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Tue, 23 Feb 2016 13:22:40 +0100
Subject: Breaks on linking in the final stages.

---
 gn/packages/bioinformatics.scm | 36 ++++++++++++++++++++----------------
 1 file changed, 20 insertions(+), 16 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index cfc5dae..3363ea2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -35,6 +35,7 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages ruby)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tbb)
   #:use-module (gnu packages textutils)
@@ -310,22 +311,19 @@ and freshness without requiring additional information from the user.")
       (license license:boost1.0))))
 
 (define-public sambamba
-  (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
-  ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+  (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
     (package
       (name "sambamba")
-      (version (string-append "0.5.9-" commit))
+      (version (string-append "0.5.9-1." (string-take commit 7)))
       (source (origin
         (method git-fetch)
         (uri (git-reference                
-              ;; https://github.com/pjotrp/sambamba.git
-              (url "https://github.com/roelj/sambamba.git")
+              (url "https://github.com/pjotrp/sambamba.git")
               (commit commit)))
-        (file-name (string-append name "-" (string-take commit 7)))
+        (file-name (string-append name "-" version "-checkout"))
         (sha256
          (base32
-          ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
-          "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"))))
+          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
       (build-system gnu-build-system)
       ;; (inputs
       ;;  `(("ldc" ,ldc)
@@ -340,13 +338,16 @@ and freshness without requiring additional information from the user.")
          ("lz4" ,lz4)
          ("rdmd" ,rdmd)
          ("zlib" ,zlib)
+         ("perl" ,perl) ; Needed for htslib
+         ("ruby" ,ruby) ; Needed for htslib
+         ("python" ,python) ; Needed for htslib
          ("gcc" ,gcc)
          ("lz4-src"
           ,(origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/Cyan4973/lz4/archive/r131.tar.gz"))
-             (file-name "lz4-131.tar.gz")
+             (file-name "lz4-r131.tar.gz")
              (sha256
               (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx"))))
          ("htslib-src"
@@ -354,7 +355,7 @@ and freshness without requiring additional information from the user.")
              (method url-fetch)
              (uri (string-append
                    "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (file-name "htslib-0.2.0-rc10.tar.gz")
              (sha256
               (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
          ("biod-src"
@@ -363,15 +364,16 @@ and freshness without requiring additional information from the user.")
              (uri (git-reference
                    (url "https://github.com/biod/BioD.git")
                    (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
+             (file-name "biod-src")
              (sha256
-              (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
-             (file-name "biod-src")))))
+              (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))))))
       (arguments
        `(#:tests? #f
-         #:make-flags (list "CC=gcc" "D_COMPILER=ldc2")
+         ;;#:make-flags 
          #: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
@@ -384,14 +386,16 @@ and freshness without requiring additional information from the user.")
                     (with-directory-excursion "lz4"
                       (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
                                       "--strip-components=1")))
-                    (zero? (system* "ln" "--symbolic" (assoc-ref inputs "biod-src") "BioD")))))
+                    (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.
            (replace
             'build
-            (lambda* (#:key inputs #:allow-other-keys)
-              (zero? (system* "make" "sambamba-ldmd2-64")))))))
+            (lambda* (#:key inputs make-flags #:allow-other-keys)
+              (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2")))))))
       (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 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/packages/bioinformatics.scm')

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/packages/bioinformatics.scm')

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 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/packages/bioinformatics.scm')

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/packages/bioinformatics.scm')

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/packages/bioinformatics.scm')

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/packages/bioinformatics.scm')

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/packages/bioinformatics.scm')

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 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/packages/bioinformatics.scm')

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