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authorpjotrp2016-03-03 14:04:12 +0000
committerpjotrp2016-03-03 14:04:12 +0000
commite6c2e0459a71e6c0fc108bf34bee94c1b59c983b (patch)
tree96fd990a74097e1a338f7bba2870fe90f6dfde5c /gn
parente1a0ed2f5ded6824db738916928d5f76226aeb8c (diff)
downloadguix-bioinformatics-e6c2e0459a71e6c0fc108bf34bee94c1b59c983b.tar.gz
Added genenetwork2-files-small
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/genenetwork.scm46
1 files changed, 42 insertions, 4 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index aec305b..54c9fce 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
@@ -141,7 +140,7 @@
(license license:agpl3+))))
(define-public genenetwork2
- (let ((commit "8c9de7e5a2016f1e5b7397be1a8e84396e3a25c5"))
+ (let ((commit "3d55e84c81ae6c10765c79b6dfa18ccf30e98b53"))
(package
(name "genenetwork2")
(version (string-append "2.0-" (string-take commit 7) ))
@@ -149,12 +148,12 @@
(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 "-" (string-take commit 7)))
(sha256
(base32
- "1kgigzs4rs6zgbqbnm40rcljzz9prlwv7n2n9an57jk58bjgf6v8"))))
+ "0pmf96hsmxpiczkh4c2zpq5zz6byklhw4vjrazn9qvrgh78aqyab"))))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
@@ -204,6 +203,45 @@
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
+(define-public genenetwork2-files-small
+ (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"))
+ ;; (targetdir (string-append out "/gn2_data_s"))
+ )
+ (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 ;; (mkdir targetdir)
+ (zero? (system* lz4unpack source "-d" "xx.tar"))
+ (zero? (system* tar "xf" "xx.tar"))
+ (copy-recursively "gn2_data_s" (string-append out "/gn2_data_s"))
+ ))))))
+ (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