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authorpjotrp2017-07-09 11:52:02 +0000
committerpjotrp2017-07-09 11:52:02 +0000
commit5870720799d5825d1e4a7e6bd7dbf14a99812097 (patch)
tree2f733aa1146660183c8580ba9864dd62770d16fe /gn
parentbdaf5cd6c71e98139c63360a345ab51e25ebc5fa (diff)
downloadguix-bioinformatics-5870720799d5825d1e4a7e6bd7dbf14a99812097.tar.gz
Update gemma and shunit2 packages
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/gemma.scm28
-rw-r--r--gn/packages/genenetwork.scm30
-rw-r--r--gn/packages/shell.scm12
3 files changed, 62 insertions, 8 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 3c40317..9986bf5 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -63,28 +63,42 @@
#:use-module (srfi srfi-1))
(define-public gemma-git ; guix candidate
- (let ((commit "5675bdf0422f63f81752bb1fcf7b436bc30bf9b7"))
+ (let ((commit "c978835c3630286414df6076d38aad16277cdb6b"))
(package
(name "gemma-git")
- (version (string-append "0.95.2a" commit ))
+ (version (string-append "0.97-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/xiangzhou/GEMMA")
+ (url "https://github.com/genenetwork/GEMMA")
(commit commit)))
(file-name (string-append name "-" commit))
(sha256
(base32
- "0qc8dx8m4cqggnin2vsbc9l91ay6h04l0mpjv8z0wcickqb4lby6"))))
+ "1hw8y7vka79v84lv5vyhkinx864yjh1wd8vfd16cvqs1bi8qw3n2"))))
(inputs `(
("gsl" ,gsl)
+ ("eigen" ,eigen)
("lapack" ,lapack)
+ ("openblas" ,openblas)
("zlib" ,zlib)
))
+ (native-inputs ; for running tests
+ `(("shunit2" ,shunit2)
+ ("which" ,which)
+ ))
+
(build-system gnu-build-system)
(arguments
- `(#:make-flags '(" FORCE_DYNAMIC=1")
+ `(#:make-flags
+ (list
+ (string-append "EIGEN_INCLUDE_PATH="
+ (assoc-ref %build-inputs "eigen")
+ "/include/eigen3/")
+ "FORCE_DYNAMIC=1"
+ "WITH_OPENBLAS=1")
#:phases
+ ; "/include/eigen3/"
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'bin-mkdir
@@ -95,8 +109,8 @@
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/gemma" (string-append out "/bin"))))))
- #:tests? #f))
- (home-page "")
+ #:parallel-tests? #f))
+ (home-page "http://www.xzlab.org/software.html")
(synopsis "Tool for genome-wide efficient mixed model association")
(description "GEMMA is the software implementing the Genome-wide
Efficient Mixed Model Association algorithm for a standard linear
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 08a8954..34178b5 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -91,7 +91,32 @@
(description #f)
(license #f)))
-(define-public qtlreaper ; guix obsolete - but used in GN2
+(define-public qn-server ; guix obsolete - but used in GN2
+ (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
+ (package
+ (name "qn-server")
+ (version (string-append "1.1-gn2-" (string-take commit 7) ))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ ;; (url "https://github.com/genenetwork/genenetwork2.git")
+ (url "https://github.com/pjotrp/QTLreaper.git")
+ (commit commit)))
+ (file-name (string-append name "-" (string-take commit 7)))
+ (sha256
+ (base32
+ "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f)) ; no 'setup.py test' really!
+ (home-page "")
+ (synopsis "GeneNetwork REST API")
+ (description
+"")
+ (license license:gpl2+))))
+
+(define-public qtlreaper
(let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
(package
(name "qtlreaper")
@@ -143,6 +168,7 @@ location of a putative QTL.")
("python" ,python-2) ;; probably superfluous
("git" ,git)
("which" ,which)
+ ("grep" ,grep)
("r" ,r)
("r-ctl" ,r-ctl)
("r-phewas" ,r-phewas)
@@ -198,6 +224,8 @@ location of a putative QTL.")
(("echo") (which "echo"))
(("redis-server") (which "redis-server"))
(("git") (which "git"))
+ (("grep") (which "grep"))
+ (("rm") (which "rm"))
(("which") (which "which")) ; three wiches in a row!
)#t))
(add-before 'install 'fix-paths
diff --git a/gn/packages/shell.scm b/gn/packages/shell.scm
index e457dce..eb9178f 100644
--- a/gn/packages/shell.scm
+++ b/gn/packages/shell.scm
@@ -3,6 +3,7 @@
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (guix git-download)
#:use-module ((guix licenses) #:prefix license:)
)
@@ -20,6 +21,9 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32 "11savxc6qliqv25kv59qak6j7syjv95hbpmq1szn1mzn32g2gc25"))))
+ (inputs `(
+ ("coreutils" ,coreutils) ; for mktemp and od
+ ))
(build-system gnu-build-system)
(arguments
`(
@@ -28,6 +32,14 @@
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
+ (add-after 'unpack 'replace-binary-paths
+ (lambda _
+ (substitute* "source/2.0/src/shell/shunit2"
+ (("/bin/sh") (which "sh"))
+ (("exec mktemp") (string-append "exec " (which "mktemp")))
+ (("/usr/bin/od") (which "od"))
+ )#t))
+
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))