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authorpjotrp2018-03-22 08:14:04 +0000
committerpjotrp2018-03-22 08:14:04 +0000
commitdb02f79948482d4060afcce4ddb69efeabf1b465 (patch)
treed3c72aaca8155de1d2d48f0c458afa91614e4c68
parent1a9a3e4964c7fa88e79bdf10b294350339ed8974 (diff)
downloadguix-bioinformatics-db02f79948482d4060afcce4ddb69efeabf1b465.tar.gz
Added qtlreaper for Python3fred
-rw-r--r--gn/packages/genenetwork.scm48
1 files changed, 44 insertions, 4 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 5217f65..9aa723f 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -133,10 +133,10 @@
(description "REST Server")
(license license:agpl3+))))
-(define-public qtlreaper
+(define-public python2-qtlreaper
(let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
(package
- (name "qtlreaper")
+ (name "python2-qtlreaper")
(version (string-append "1.1-gn2-" (string-take commit 7) ))
(source (origin
(method git-fetch)
@@ -166,6 +166,46 @@ bootstrap resampling to estimate the confidence region for the
location of a putative QTL.")
(license license:gpl2+))))
+(define-public python-qtlreaper
+ (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
+ (package
+ (name "python-qtlreaper")
+ (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
+ `(
+ #:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'unpack 'fix-tests
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("./test/example1.py" "./test/example2.py")
+ (("/usr/bin/python") (which "python3"))))))
+ #:tests? #f)) ; no 'setup.py test' really!
+ (home-page "http://qtlreaper.sourceforge.net/")
+ (synopsis "Scan expression data for QTLs")
+ (description
+ "Batch-oriented version of WebQTL. It requires, as input,
+expression data from members of a set of recombinant inbred lines and
+genotype information for the same lines. It searches for an
+association between each expression trait and all genotypes and
+evaluates that association by a permutation test. For the permutation
+test, it performs only as many permutations as are necessary to define
+the empirical P-value to a reasonable precision. It also performs
+bootstrap resampling to estimate the confidence region for the
+location of a putative QTL.")
+ (license license:gpl2+))))
+
(define-public genenetwork2
(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
(package
@@ -231,7 +271,7 @@ location of a putative QTL.")
("python2-pyyaml" ,python2-pyyaml)
("python2-unittest2" ,python2-unittest2)
("python2-xlsxwriter" ,python2-xlsxwriter)
- ("qtlreaper" ,qtlreaper)
+ ("python2-qtlreaper" ,python2-qtlreaper)
("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
))
(build-system python-build-system)
@@ -418,7 +458,7 @@ location of a putative QTL.")
;; Without Python3 support
- ("qtlreaper" ,qtlreaper) ;; Run as an external program
+ ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program
("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program
("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program
("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)