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authorRoel Janssen2016-02-22 10:44:54 +0100
committerRoel Janssen2016-02-22 10:44:54 +0100
commit840ff7f96e50cb9e58832c573ce3a9b05a2888c9 (patch)
tree2a29eb52d435f640e72997d44f47e99be32bae8c
parent03ebb3b1a374406039494bdf5d0cb1493ddb97d8 (diff)
parent520b002306561ed81599ddfed18f9662b99d5846 (diff)
downloadguix-bioinformatics-840ff7f96e50cb9e58832c573ce3a9b05a2888c9.tar.gz
Synchronise with upstream.
-rw-r--r--gn/packages/bioinformatics.scm185
-rw-r--r--gn/packages/genenetwork.scm204
-rw-r--r--gn/packages/statistics.scm40
3 files changed, 264 insertions, 165 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1b4680e..80fe134 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)
@@ -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)
@@ -44,47 +44,9 @@
#: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")
@@ -306,117 +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)
- ("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
(let ((commit "4dba6877c481c1a911a7d50714da8fbd80022f0e"))
(package
@@ -461,17 +312,20 @@ and freshness without requiring additional information from the user.")
(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)
@@ -514,16 +368,17 @@ and freshness without requiring additional information from the user.")
;; 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
@@ -532,7 +387,7 @@ 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
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+))))