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authorpjotrp2016-01-22 11:57:01 +0300
committerpjotrp2016-01-22 11:57:01 +0300
commitbd27d282ef25ae04daa3ef7ef8413b5fedce527d (patch)
tree01ed61883e529cc244763b509f270fbb6ee99d3c /gn/packages
parentb88ec82e4de27f370a10bc41b9403780b7b30768 (diff)
downloadguix-bioinformatics-bd27d282ef25ae04daa3ef7ef8413b5fedce527d.tar.gz
add qtlreaper
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm35
1 files changed, 35 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 787c2a9..43befb4 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -120,6 +120,41 @@
"Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules 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 genenetwork2
(let ((commit "9e9475053"))