diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 91 |
1 files changed, 90 insertions, 1 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3051dcb..553fbd7 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -7,6 +7,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) + #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) #:use-module (guix build-system perl) #:use-module (guix build-system python) @@ -20,6 +21,9 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages check) + #:use-module (gnu packages cran) + #:use-module (gn packages crates-io) + #:use-module (gnu packages crates-io) #:use-module (gnu packages databases) #:use-module (gnu packages cpio) #:use-module (gn packages elixir) @@ -53,6 +57,7 @@ #:use-module (gn packages javascript) #:use-module (gn packages phewas) #:use-module (gn packages python) + #:use-module (gn packages python24) #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) @@ -167,6 +172,41 @@ bootstrap resampling to estimate the confidence region for the location of a putative QTL.") (license license:gpl2+)))) +(define-public python24-qtlreaper + (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) + (package + (name "python24-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 + "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2.4 + #:tests? #f)) ; no 'setup.py test' really! + (native-inputs + `(("python24-setuptools" ,python24-setuptools))) + (home-page "http://qtlreaper.sourceforge.net/") + (synopsis "Scan 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 python-qtlreaper (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) (package @@ -207,6 +247,55 @@ bootstrap resampling to estimate the confidence region for the location of a putative QTL.") (license license:gpl2+)))) +(define-public rust-qtlreaper + (let ((commit "eacf6ff1c3d1cd16084a70a7a425bd77080c15de") + (revision "1")) + (package + (name "rust-qtlreaper") + (version (git-version "0.1.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chfi/rust-qtlreaper.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gr2z54i11zz94ra4w06fhfnwnmmhl5xyc8qhlk0v2qq18yfi7ji")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rand" ,rust-rand-0.6) + ("rust-structopt" ,rust-structopt) + ("rust-rayon" ,rust-rayon-1.0) + ("rust-serde" ,rust-serde) + ("rust-serde-json" ,rust-serde-json)) + #:phases + (modify-phases %standard-phases + (add-after 'configure 'regenerate-cargo-lock + (lambda _ + (delete-file "Cargo.lock") + (invoke "cargo" "generate-lockfile"))) + (add-after 'patch-generated-file-shebangs 'patch-cargo-checksums + (lambda _ + (use-modules (guix build cargo-utils)) + (for-each + (lambda (filename) + (use-modules (guix build cargo-utils)) + (delete-file filename) + (let* ((dir (dirname filename))) + (display (string-append + "patch-cargo-checksums: generate-checksums for " + dir "\n")) + (generate-checksums dir))) + (find-files "guix-vendor" ".cargo-checksum.json")) + #t))))) + (home-page "https://github.com/chfi/rust-qtlreaper") + (synopsis "Reimplementation of genenetwork/QTLReaper in Rust") + (description "Reimplementation of genenetwork/QTLReaper in Rust") + (license #f)))) + (define-public genenetwork2 (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) (package @@ -247,7 +336,7 @@ location of a putative QTL.") ("python2-pillow" ,python2-pillow) ("python2-cssselect" ,python2-cssselect) ("python2-elasticsearch" ,python2-elasticsearch) - ("python2-htmlgen-gn" ,python2-htmlgen-gn) + ("python2-htmlgen" ,python2-htmlgen) ("python2-jinja2" ,python2-jinja2) ("python2-sqlalchemy" ,python2-sqlalchemy) ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) |