diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 35 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 36 | ||||
| -rw-r--r-- | gn/packages/python.scm | 2 | ||||
| -rw-r--r-- | gn/packages/statistics.scm | 28 |
4 files changed, 64 insertions, 37 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..dfbba02 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -87,6 +87,41 @@ (description #f) (license #f))) +(define-public qtlreaper + (let ((commit "71fbbe2b35e4f54937be2d54d09fb71d25fe5fad")) + (package + (name "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 + "0g0v20lh7773cm2xdqz6xzwjw4130y265n79z5x20p5aja5y5kmg")))) + (build-system python-build-system) + ;; (native-inputs + ;; `(("python-setuptools" ,python-setuptools))) + (arguments + `(#:python ,python-2 + )) + (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 @@ -157,6 +192,7 @@ (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) + ("r-ctl" ,r-ctl) ("r-wgcna" ,r-wgcna) ("r-qtl" ,r-qtl) ("redis" ,redis) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index e4196cf..7dbd968 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -396,7 +396,7 @@ version ".tgz")) (native-inputs `(("python2-setuptools" ,python2-setuptools))) (propagated-inputs - `(("python2-pillow" ,python2-pillow))) + `(("python2-pil" ,python2-pil))) (arguments `( #:python ,python-2 diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index dbe6b99..b83ccf2 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -14,6 +14,7 @@ #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) @@ -333,7 +334,7 @@ (uri (git-reference (url "https://github.com/genenetwork/pylmm.git") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" commit)) (sha256 (base32 "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964")))) @@ -362,3 +363,28 @@ (description "Fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).") (license license:agpl3+)))) + +(define-public r-ctl + (package + (name "r-ctl") + (version "1.0.0-0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cran/src/contrib/ctl_" + version ".tar.gz")) + (sha256 + (base32 + "12hrrql9wz43s1d3sfyzlqzx7ajrl3hvf96776ik6icbm8by8h6j")))) + (build-system r-build-system) + (inputs `( + ("r-qtl" ,r-qtl) + )) + (home-page "https://github.com/DannyArends/CTLmapping") + (synopsis "R package for analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL)") + (description "Analysis of experimental crosses to identify genetic +markers associated with correlation changes in quantitative +traits (CTL). The additional correlation information obtained can be +combined with QTL information to perform de novo reconstruction of +interaction networks.") + (license license:gpl3))) |