diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 25 |
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") |