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authorpjotrp2017-05-19 08:34:41 +0000
committerpjotrp2017-05-19 08:34:41 +0000
commit166feefc6b86abaac83509b2607f7e2842c39c5d (patch)
tree8eb0fb0e3e3cd4315eb77c0f562ffe9189bf1742
parent0d46a521faaaa121687bb634ba0388de83825048 (diff)
downloadguix-bioinformatics-166feefc6b86abaac83509b2607f7e2842c39c5d.tar.gz
genenetwork2: patching paths of depndencies
-rw-r--r--gn/packages/genenetwork.scm26
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" ))