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-rw-r--r--gn/packages/genenetwork.scm60
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!