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authorEfraim Flashner2019-07-04 09:19:11 -0500
committerEfraim Flashner2019-07-04 09:19:11 -0500
commitd88288b63ba5c78d0af762fe72be2f4fd6315350 (patch)
treec79cd0cda755c1f18c41d9c3e51b11bdb1dd66f8 /gn
parent1647ee8c2f317d7c68ad1116741f931d0d1ebd5a (diff)
downloadguix-bioinformatics-d88288b63ba5c78d0af762fe72be2f4fd6315350.tar.gz
gn: Add python24-qtlreaper.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/genenetwork.scm36
1 files changed, 36 insertions, 0 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 987cf61..4386aff 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -54,6 +54,7 @@
#:use-module (gn packages javascript)
#:use-module (gn packages phewas)
#:use-module (gn packages python)
+ #:use-module (gn packages python24)
#:use-module (gn packages statistics)
#:use-module (srfi srfi-1))
@@ -168,6 +169,41 @@ bootstrap resampling to estimate the confidence region for the
location of a putative QTL.")
(license license:gpl2+))))
+(define-public python24-qtlreaper
+ (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
+ (package
+ (name "python24-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
+ `(#:python ,python-2.4
+ #:tests? #f)) ; no 'setup.py test' really!
+ (native-inputs
+ `(("python24-setuptools" ,python24-setuptools)))
+ (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 python-qtlreaper
(let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
(package