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-rw-r--r--gn/packages/genenetwork.scm78
1 files changed, 70 insertions, 8 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 1b52a5d..79ad3fe 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -87,7 +87,6 @@
(description #f)
(license #f)))
-
(define-public genenetwork1
(let ((commit "d622c803b"))
(package
@@ -141,26 +140,29 @@
(license license:agpl3+))))
(define-public genenetwork2
- (let ((commit "9e9475053"))
+ (let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a"))
(package
(name "genenetwork2")
- (version (string-append "2.0-" commit ))
+ (version (string-append "2.0-" (string-take commit 7) ))
(source (origin
(method git-fetch)
(uri (git-reference
;; (url "https://github.com/genenetwork/genenetwork2.git")
- (url "https://github.com/pjotrp/genenetwork2.git")
+ (url "https://github.com/genenetwork/genenetwork2_diet.git")
(commit commit)))
- (file-name (string-append name "-" commit))
+ (file-name (string-append name "-" (string-take commit 7)))
(sha256
(base32
- "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
+ "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
+ ("r-wgcna" ,r-wgcna)
+ ("r-qtl" ,r-qtl)
("redis" ,redis)
("mysql" ,mysql)
("gemma" ,gemma-git)
+ ("genenetwork2-files-small" ,genenetwork2-files-small)
("pylmm-gn2" ,pylmm-gn2)
("plink2" ,plink-ng)
("nginx" ,nginx)
@@ -178,8 +180,9 @@
("python2-pandas" ,python2-pandas)
("python2-parallel" ,python2-parallel)
("python2-passlib" ,python2-passlib)
- ("python2-piddle" ,python2-piddle)
+ ("python2-piddle-gn" ,python2-piddle-gn)
("python2-redis" ,python2-redis)
+ ("python2-pil" ,python2-pil)
("python2-requests" ,python2-requests)
("python2-rpy2" ,python2-rpy2)
("python2-scipy" ,python2-scipy)
@@ -189,11 +192,28 @@
;; python-yolk is not needed
("plink" ,plink)
("qtlreaper" ,qtlreaper)
- ("r-qtl" ,r-qtl)
))
(build-system python-build-system)
(arguments
`(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'install 'fix-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* (
+ (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
+ (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
+ (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2"))
+ (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+ )
+
+ (substitute* '("etc/default_settings.py")
+ (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
+ (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
+ (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
+ (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
+ )
+ ))))
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
@@ -203,6 +223,48 @@
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
+(define-public genenetwork2-files-small1
+ (let ((pfff "xx"))
+ (package
+ (name "genenetwork2-files-small")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
+ (file-name (string-append name "-" pfff))
+ (sha256
+ (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
+ (build-system trivial-build-system)
+ (native-inputs `(("lz4" ,lz4)
+ ("tar" ,tar)
+ ("source" ,source)))
+
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (let* ((out (assoc-ref %outputs "out"))
+ (name "gn2_data_s")
+ (tarfn (string-append name ".tar"))
+ (targetdir (string-append out "/share/genenetwork2/"))
+ )
+ (begin
+ (use-modules (guix build utils))
+ (let ((source (assoc-ref %build-inputs "source"))
+ (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4"))
+ (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
+ )
+ (and
+ (zero? (system* lz4unpack source "-d" tarfn))
+ (zero? (system* tar "xf" tarfn))
+ (mkdir-p targetdir)
+ (copy-recursively name targetdir)
+ ))))))
+ (home-page "http://genenetwork.org/")
+ (synopsis "Small file archive to run on genenetwork")
+ (description "Genenetwork genotype and mapping files.")
+ (license license:agpl3+))))
+
(define-public genenetwork2-database-small
(let ((md5 "93e745e9c"))
(package