diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 48 |
1 files changed, 44 insertions, 4 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5217f65..9aa723f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -133,10 +133,10 @@ (description "REST Server") (license license:agpl3+)))) -(define-public qtlreaper +(define-public python2-qtlreaper (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) (package - (name "qtlreaper") + (name "python2-qtlreaper") (version (string-append "1.1-gn2-" (string-take commit 7) )) (source (origin (method git-fetch) @@ -166,6 +166,46 @@ 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 + (name "python-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 + `( + #:phases + (modify-phases %standard-phases + (add-after + 'unpack 'fix-tests + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("./test/example1.py" "./test/example2.py") + (("/usr/bin/python") (which "python3")))))) + #:tests? #f)) ; no 'setup.py test' really! + (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 genenetwork2 (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) (package @@ -231,7 +271,7 @@ location of a putative QTL.") ("python2-pyyaml" ,python2-pyyaml) ("python2-unittest2" ,python2-unittest2) ("python2-xlsxwriter" ,python2-xlsxwriter) - ("qtlreaper" ,qtlreaper) + ("python2-qtlreaper" ,python2-qtlreaper) ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) )) (build-system python-build-system) @@ -418,7 +458,7 @@ location of a putative QTL.") ;; Without Python3 support - ("qtlreaper" ,qtlreaper) ;; Run as an external program + ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program ("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) |