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authorpjotrp2016-03-04 11:07:37 +0000
committerpjotrp2016-03-04 11:07:37 +0000
commit6332603b4492b36a79d0744289a50f7081a52a24 (patch)
treeb193e89ebf6685a1c46212f7e9d4d1844a9f14e1 /gn/packages
parente6c2e0459a71e6c0fc108bf34bee94c1b59c983b (diff)
downloadguix-bioinformatics-6332603b4492b36a79d0744289a50f7081a52a24.tar.gz
GN2 is now a self contained package (except for the database)
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/genenetwork.scm25
1 files changed, 18 insertions, 7 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 54c9fce..fdcbb7f 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -140,7 +140,7 @@
(license license:agpl3+))))
(define-public genenetwork2
- (let ((commit "3d55e84c81ae6c10765c79b6dfa18ccf30e98b53"))
+ (let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a"))
(package
(name "genenetwork2")
(version (string-append "2.0-" (string-take commit 7) ))
@@ -153,7 +153,7 @@
(file-name (string-append name "-" (string-take commit 7)))
(sha256
(base32
- "0pmf96hsmxpiczkh4c2zpq5zz6byklhw4vjrazn9qvrgh78aqyab"))))
+ "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
@@ -161,6 +161,7 @@
("redis" ,redis)
("mysql" ,mysql)
("gemma" ,gemma-git)
+ ("genenetwork2-files-small" ,genenetwork2-files-small)
("pylmm-gn2" ,pylmm-gn2)
("plink2" ,plink-ng)
("nginx" ,nginx)
@@ -194,6 +195,13 @@
(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" )))
+ (substitute* '("etc/default_settings.py")
+ (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )))))))
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
@@ -224,7 +232,9 @@
`(#:modules ((guix build utils))
#:builder
(let* ((out (assoc-ref %outputs "out"))
- ;; (targetdir (string-append out "/gn2_data_s"))
+ (name "gn2_data_s")
+ (tarfn (string-append name ".tar"))
+ (targetdir (string-append out "/share/genenetwork2/"))
)
(begin
(use-modules (guix build utils))
@@ -232,10 +242,11 @@
(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"))
+ (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")