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authorPjotr Prins2018-10-16 01:39:13 -0500
committerPjotr Prins2018-10-16 01:39:13 -0500
commit83963fe7ba5396855a0ce6544fd1f959235c2b79 (patch)
treee65967c9b6dc829ca56196680bb8775088251429 /gn/packages
parentbe1ffd0a57a83bdbcf08a1df773cbda0e60df688 (diff)
downloadguix-bioinformatics-83963fe7ba5396855a0ce6544fd1f959235c2b79.tar.gz
Updated gemma and openblas
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm32
-rw-r--r--gn/packages/genenetwork.scm2
2 files changed, 15 insertions, 19 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 251f86c..ec66a3d 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -63,12 +63,10 @@
(define-public openblas-git
- (let ((commit "893bd14e924fa72a4ed345a75d64c637f1b1c550"))
- ; (let ((commit "36aea5ce2d5565e006a027a23e805cd9ff0e2eee"))
+ (let ((commit "2263d3906c23bd7341ebe714ef7c44fc84b0d1d0"))
(package
(name "openblas-git")
- (version (string-append "0.2.20-git-" (string-take commit 7)))
- ; (version (string-append "0.3.1-git-" (string-take commit 7)))
+ (version (string-append "0.3.3-git-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -77,8 +75,7 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0qv03c2yq46p9sajc3a3f56ijfifyv6f4n51a81wc2hihy4ilcap"))))
- ; "1rva61y4lwi6zkja5349r59fxichdhqaqk608kklw5bwk04fjh86"))))
+ "1x2axq36szcz1gc77vcf3ypm0g1r3jwj03vq6rr94h098rcdv4s9"))))
(build-system gnu-build-system)
(arguments
@@ -144,10 +141,10 @@
(define-public gemma-gn2 ; guix candidate - generic openblas version
- (let ((commit "c760aa09c2aa91ca6270b5f898c27e9aed376a73"))
+ (let ((commit "6b1e007ea9ead6123e9d7f078f3e59054047521d"))
(package
(name "gemma-gn2")
- (version (string-append "0.97-" (string-take commit 7)))
+ (version (string-append "0.98-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -156,13 +153,13 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0s61w8av70kqvkb00znrqnr59axygh9gnlxar8rfyasr5g6xvl8w"))))
+ "0gg4rrxcjbhfqfdaljnn86yffaa0n2d2j67j2gv47wvgrnn8fvwz"))))
(inputs `(
- ("gfortran:lib" ,gfortran "lib")
+ ; ("gfortran:lib" ,gfortran "lib")
("gsl" ,gsl)
("eigen" ,eigen)
("shunit2" ,shunit2)
- ("lapack" ,lapack)
+ ; ("lapack" ,lapack)
("openblas" ,openblas)
("zlib" ,zlib)
))
@@ -178,7 +175,6 @@
(string-append "EIGEN_INCLUDE_PATH="
(assoc-ref %build-inputs "eigen")
"/include/eigen3/")
- "WITH_LAPACK=1"
)
#:phases
; "/include/eigen3/"
@@ -196,10 +192,10 @@
#: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
-mixed model and some of its close relatives for genome-wide
-association studies (GWAS).")
+ (description "Genome-wide Efficient Mixed Model Association (GEMMA)
+provides a standard linear mixed model resolver with application in
+genome-wide association studies (GWAS).")
+
(license license:gpl3))))
(define-public gemma-gn2-git ; openblas optimized
@@ -207,7 +203,7 @@ association studies (GWAS).")
(inherit gemma-gn2)
(name "gemma-gn2-git")
(inputs `(
- ("gfortran:lib" ,gfortran "lib")
+ ; ("gfortran:lib" ,gfortran "lib")
("gsl" ,gsl)
("eigen" ,eigen)
("shunit2" ,shunit2)
@@ -233,7 +229,7 @@ association studies (GWAS).")
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/gemma" (string-append out "/bin"))))))
- ; #:tests? #f
+ #:tests? #f
#:parallel-tests? #f))
))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 44fa61b..a54b557 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -210,7 +210,7 @@ location of a putative QTL.")
(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
(package
(name "genenetwork2")
- (version (string-append "2.10rc5-" (string-take commit 7) ))
+ (version (string-append "2.11-guix-" (string-take commit 7) ))
(source (origin
(method git-fetch)
(uri (git-reference