diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 60 |
1 files changed, 35 insertions, 25 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3507064..b534ae7 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -84,30 +84,40 @@ 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, + (let ((commit "442c217b90393380a8634ff8636b44992f5c53dd")) + (package + (name "python24-qtlreaper") + (version (git-version "1.11" "gn1" commit)) + (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 (git-file-name name version)) + (sha256 + (base32 + "1rrbm1ap2zzyjxmrs9aa1d18sgiba5dhj1fmkl7wmab06jv3j1hm")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2.4 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-max-markername-size-larger + (lambda _ + (substitute* "Src/dataset.c" + (("512") "2048")) + #t)) + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "python" "test/runtest.py")))))) + (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 @@ -116,7 +126,7 @@ 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+)))) + (license license:gpl2+)))) ;; Reintroduced python2-gunicorn because we are running GN with python2 ;; right now. Please keep it until we migrate to Python3 fully! |