From e472db7bd929f8b511b0cd5e777dff25c1fbc692 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 20 Feb 2016 13:03:51 +0000
Subject: Added package for pylmm

---
 gn/packages/statistics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

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

diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 065826e..c10ba29 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -148,3 +148,27 @@
      "R/lmmlite")
     (home-page "https://github.com/kbroman/")
     (license license:asl2.0)))
+
+(define-public pylmm-gn2
+  (let ((commit "f5c9e2378"))
+  (package
+    (name "pylmm-gn2")
+    (version (string-append "1.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/genenetwork/pylmm.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "10qb5dpwqjdiq9gakl7m4p4ckjlc701mzqpgbhp89w1aysddj1c7"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test'
+    (home-page "http://genenetwork.org/")
+    (synopsis "LMM resolver")
+    (description "Fast and lightweight linear mixed-model (LMM) solver
+for use in genome-wide association studies (GWAS).")
+    (license license:agpl3+))))
-- 
cgit v1.2.3


From dfb685956526dce67a8e03849bffd1d9d52c5958 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 20 Feb 2016 14:18:45 +0000
Subject: pylmm: Patch wrapper script so it points to the correct locations.

---
 gn/packages/statistics.scm | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

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

diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index c10ba29..2d83816 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -150,7 +150,7 @@
     (license license:asl2.0)))
 
 (define-public pylmm-gn2
-  (let ((commit "f5c9e2378"))
+  (let ((commit "3c6d1cac8"))
   (package
     (name "pylmm-gn2")
     (version (string-append "1.0-" commit ))
@@ -162,11 +162,27 @@
              (file-name (string-append name "-" commit)) 
              (sha256
               (base32
-               "10qb5dpwqjdiq9gakl7m4p4ckjlc701mzqpgbhp89w1aysddj1c7"))))
+               "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964"))))
     (build-system python-build-system)
+    (inputs `(
+              ("python2-setuptools" ,python2-setuptools)
+              ("python2-scipy" ,python2-scipy)
+              ("python2-numpy" ,python2-numpy)
+              ))
     (arguments
      `(#:python ,python-2
-       #:tests? #f))   ; no 'setup.py test'
+       #:tests? #f        ; no 'setup.py test'
+       #:phases
+       (modify-phases %standard-phases
+         (add-before
+          'build 'change-paths
+          (lambda* (#:key outputs #:allow-other-keys)
+                   (let ((out (assoc-ref outputs "out")))
+                     (substitute* "scripts/pylmm_redis"
+                                  (("/usr/bin/python") (which "python"))
+                                  (("\\$PACKAGEDIR") (string-append out "/lib/python2.7/site-packages")))
+                     ))))))
+
     (home-page "http://genenetwork.org/")
     (synopsis "LMM resolver")
     (description "Fast and lightweight linear mixed-model (LMM) solver
-- 
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/statistics.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/statistics.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 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/packages/statistics.scm')

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