diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 58 |
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"))))) |