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authorpjotrp2016-09-29 08:51:42 +0000
committerpjotrp2016-09-29 08:51:42 +0000
commit9351ff09f6ac8c557ce3e847518f04f281e7b3dc (patch)
treed21e302bdd7c1dc6dfc52206c843e415d72ddc43 /gn
parente73d1d766905b5f98f68d1799a88a3b86c1ff9f9 (diff)
downloadguix-bioinformatics-9351ff09f6ac8c557ce3e847518f04f281e7b3dc.tar.gz
Move qtlreaper to genenetwork.scm
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm35
-rw-r--r--gn/packages/genenetwork.scm35
2 files changed, 35 insertions, 35 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index f62949d..b509fc3 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -772,41 +772,6 @@ to sample traits. Also includes a number of utility functions for
data manipulation and visualization.")
(license license:gpl2+))))
-(define-public qtlreaper
- (package
- (name "qtlreaper")
- (version "1.1.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz"
- ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb"))
- ))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x"))))
- (build-system python-build-system)
- ;; (native-inputs
- ;; `(("python-setuptools" ,python-setuptools)))
- (arguments
- `(#:python ,python-2
- #:tests? #f)) ; no 'setup.py test'
- (home-page "http://qtlreaper.sourceforge.net/")
- (synopsis "Tool for scanning expression data for QTLs")
- (description
- "It is essentially the 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 plink2
(package
(name "plink2")
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index a7317c6..d8a1813 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -87,6 +87,41 @@
(description #f)
(license #f)))
+(define-public qtlreaper
+ (package
+ (name "qtlreaper")
+ (version "1.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz"
+ ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb"))
+ ))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x"))))
+ (build-system python-build-system)
+ ;; (native-inputs
+ ;; `(("python-setuptools" ,python-setuptools)))
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f)) ; no 'setup.py test'
+ (home-page "http://qtlreaper.sourceforge.net/")
+ (synopsis "Tool for scanning 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 genenetwork1
(let ((commit "d622c803b"))
(package