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authorEfraim Flashner2019-09-11 06:37:44 -0500
committerEfraim Flashner2019-09-11 06:37:44 -0500
commit8ddd60a8628fb389a2a564942c2e5196537141b3 (patch)
tree113729413e8db8a851ccad79c3301c54e5506e8e /gn
parente31d46f821048cbde3ab1cefb09cc9d734123d82 (diff)
downloadguix-bioinformatics-8ddd60a8628fb389a2a564942c2e5196537141b3.tar.gz
gn: Add qctool.
* gn/packages/bioinformatics.scm (qctool): New variable.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm58
1 files changed, 58 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a28ceb8..726eed2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -6,9 +6,11 @@
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
+ #:use-module (guix hg-download)
#:use-module (guix build-system ant)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system waf)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages bioinformatics)
@@ -20,6 +22,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages readline)
#:use-module (gnu packages statistics))
(define-public contra
@@ -658,3 +661,58 @@ the \"safe\" merging of many files from many individuals into one stream,
suitable for input into downstream processing systems such as freebayes (
population variant detector).")
(license #f)))) ; no license listed
+
+(define-public qctool
+ (let ((changeset "73662f5f6e1e6efe75796bc64e342fb5d5d35e54") ; May 30, 2019
+ (revision "1"))
+ (package
+ (name "qctool")
+ (version (string-append "2.0.5-" revision "." (string-take changeset 7)))
+ (source
+ (origin
+ (method hg-fetch)
+ (uri (hg-reference
+ (url "https://bitbucket.org/gavinband/qctool")
+ (changeset changeset)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32 "0lcir6jdw1gsi1l0yrsyqgrb8dryxxw3gyncfx5bx34qbhd6f5dv"))))
+ (build-system waf-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f ; no check command
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'rename-waf
+ (lambda _
+ (rename-file "waf-1.5.18" "waf")
+ #t)))))
+ (native-inputs
+ `(("readline" ,readline)
+ ("zlib" ,zlib)))
+ (inputs
+ `(("lapack" ,lapack)
+ ("openblas" ,openblas)))
+ (home-page "https://www.well.ox.ac.uk/~gav/qctool_v2/")
+ (synopsis "Quality control and analysis of gwas datasets")
+ (description
+ "QCTOOL is a command-line utility program for manipulation and quality
+control of gwas datasets and other genome-wide data. QCTOOL can be used
+@enumerate
+@item To compute per-variant and per-sample QC metrics.
+@item To filter out samples or variants.
+@item To merge datasets in various ways.
+@item To convert dataset between file formats. (In particular QCTOOL can read
+and write BGEN files, including full support for the BGEN v1.2 format that has
+been used for the UK Biobank imputed data full release).
+@item To manipulate datasets in various ways - e.g. by updating data fields or
+aligning alleles to a reference sequence based on information in a strand file.
+@item To annotate variants with information from BED files, sequence from FASTA
+files, or with genetic map positions.
+@item To compute LD metrics between variants.
+@item To compare genotypes for individuals typed or imputed or phased in
+different datasets.
+@item To compute between-sample relatedness and principal components.
+@item To compute 'genetic risk predictor' scores.
+@end enumerate")
+ (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))))