diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 26 |
1 files changed, 21 insertions, 5 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 70cb928..14ac8df 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages xml) #:use-module (gnu packages zip) #:use-module (gnu packages bootstrap) + #:use-module (gnu packages version-control) #:use-module (gn packages bioinformatics) #:use-module (gn packages gemma) #:use-module (gn packages javascript) @@ -124,22 +125,23 @@ location of a putative QTL.") (license license:gpl2+)))) (define-public genenetwork2 - (let ((commit "5fa50d0779ea8a8713b0fba9ee45ecd50e6f28e3")) + (let ((commit "93e1b740a5503d9c29c058e9f0c99e6b7396f1c0")) (package (name "genenetwork2") - (version (string-append "2.10rc2-" (string-take commit 7) )) + (version (string-append "2.10rc3-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) - (file-name (string-append name "-" (string-take commit 7))) + (file-name (string-append name "-" version)) (sha256 (base32 - "1z674057hcmfv58b0k2v4n1wgcrnfpshpr3xhm2nchwm22lq8krw")))) + "1a3j7a4bpfki44w57wlk8qm51wkcvj2kjp95rk64n3in25l8w3x9")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous + ("git" ,git) ("r" ,r) ("r-ctl" ,r-ctl) ("r-phewas" ,r-phewas) @@ -183,6 +185,20 @@ location of a putative QTL.") #:phases (modify-phases %standard-phases (delete 'reset-gzip-timestamps) + (add-after 'unpack 'fix-paths-scripts + (lambda* _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python2") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + ; (("read") (which "read")) + )#t)) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ( @@ -193,7 +209,7 @@ location of a putative QTL.") ) (substitute* '("etc/default_settings.py") - (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) + (("^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" )) |