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-rw-r--r--gn/packages/bioinformatics.scm386
-rw-r--r--gn/packages/genenetwork.scm204
-rw-r--r--gn/packages/statistics.scm40
3 files changed, 375 insertions, 255 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index b7384ef..3363ea2 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)
@@ -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)
@@ -44,47 +45,9 @@
#: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 r-wgcna
(package
(name "r-wgcna")
@@ -305,230 +268,143 @@ 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 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))
+(define-public sambamba
+ (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+ (package
+ (name "sambamba")
+ (version (string-append "0.5.9-1." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjotrp/sambamba.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (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)
+ ("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-r131.tar.gz")
(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
+ (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")
+ (sha256
+ (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
+ ("biod-src"
+ ,(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))
+ (url "https://github.com/biod/BioD.git")
+ (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
+ (file-name "biod-src")
(sha256
- (base32
- "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
- (propagated-inputs `( ;; propagated for development purposes
- ("python" ,python-2) ;; probably superfluous
- ("r" ,r)
- ("redis" ,redis)
- ("mysql" ,mysql)
- ("gemma" ,gemma-git)
- ("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")
- (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)))
-
-(define-public sambamba
- (package
- (name "sambamba")
- (version "0.5.9")
- (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"))))
- (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" "sambamba-ldmd2-64" 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"))))))
+ (arguments
+ `(#:tests? #f
+ ;;#: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
+ ;; 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")))
+ (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 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
+ "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
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
new file mode 100644
index 0000000..2f755a6
--- /dev/null
+++ b/gn/packages/genenetwork.scm
@@ -0,0 +1,204 @@
+;; 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 bioinformatics)
+ #: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+))))
+
+;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
+;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 065826e..2d83816 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -148,3 +148,43 @@
"R/lmmlite")
(home-page "https://github.com/kbroman/")
(license license:asl2.0)))
+
+(define-public pylmm-gn2
+ (let ((commit "3c6d1cac8"))
+ (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
+ "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'
+ #: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
+for use in genome-wide association studies (GWAS).")
+ (license license:agpl3+))))