diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 8 | ||||
| -rw-r--r-- | gn/packages/hyphy.scm | 5 | ||||
| -rw-r--r-- | gn/packages/python.scm | 16 | ||||
| -rw-r--r-- | gn/packages/ruby.scm | 4 | ||||
| -rw-r--r-- | gn/packages/statistics.scm | 40 |
5 files changed, 9 insertions, 64 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4450bfa..8c28a85 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -240,7 +240,6 @@ location of a putative QTL.") ("gemma-wrapper" ,gemma-wrapper) ("genenetwork2-files-small" ,genenetwork2-files-small) ("plink-ng-gn" ,plink-ng-gn) - ("pylmm-gn2" ,pylmm-gn2) ("nginx" ,nginx) ("python2-flask" ,python2-flask) ("gunicorn" ,gunicorn) @@ -265,7 +264,8 @@ location of a putative QTL.") ;; ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) - ; ("python2-pil1" ,python2-pil1) ; should move to pillow some day + ; ("python2-pil1" ,python2-pil1) ; merged to pillow (https://github.com/genenetwork/genenetwork2/pull/355) + ("python2-pillow" ,python2-pillow) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) @@ -306,14 +306,14 @@ location of a putative QTL.") (lambda* (#:key inputs #:allow-other-keys) (let* ( (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) - (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) ) (substitute* '("etc/default_settings.py") (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) + ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) ) diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm index e5c120a..3902a8b 100644 --- a/gn/packages/hyphy.scm +++ b/gn/packages/hyphy.scm @@ -58,11 +58,6 @@ `(("python" ,python-2) ("fftw-openmpi" ,fftw-openmpi))) (build-system cmake-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "make" "MPI"))))))) (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") #:tests? #f)) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 651a635..adb814f 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -70,7 +70,7 @@ (define-public python2-rpy2 (package (name "python2-rpy2") - (version "2.7.6") + (version "2.7.6") ; Python2 compatible version (source (origin (method url-fetch) @@ -80,17 +80,8 @@ "0nhan2qvrw7b7gg5zddwa22kybdv3x1g26vkd7q8lvnkgzrs4dga")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; apparently incompatible with Python 3 - #:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'check) - (add-after 'install 'check - (lambda* (#:key outputs inputs #:allow-other-keys) - ;; It's easier to run tests after install. - ;; Make installed package available for running the tests - (add-installed-pythonpath inputs outputs) - (zero? (system* "python" "-m" "rpy2.tests" "-v"))))))) + `(#:python ,python-2 ; we are still using Python2 + #:tests? #f)) (propagated-inputs `(("python2-six" ,python2-six) ("python2-singledispatch" ,python2-singledispatch) @@ -730,7 +721,6 @@ the older versions.") (base32 "1rc8kf72v180qlygkh1y0jwv2fxqpx7n97bqfhbwgnn31iwai9g3")))) (build-system python-build-system) - (build-system python-build-system) (propagated-inputs `( ("python-more-itertools" ,python-more-itertools) diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm index 3838d55..82360ff 100644 --- a/gn/packages/ruby.scm +++ b/gn/packages/ruby.scm @@ -254,8 +254,8 @@ for an example.") ("ruby-nokogiri" ,ruby-nokogiri) ("ruby-ntlm-http" ,ruby-ntlm-http) ("ruby-webrobots" ,ruby-webrobots))) - (arguments - `(#:tests? #f)) ;; one test fails + ; (arguments + ; `(#:tests? #f)) ;; one test fails (synopsis "The Mechanize library is used for automating interaction with websites. Mechanize automatically stores and sends cookies, follows redirects, diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index edc9ab7..459e0d1 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -275,46 +275,6 @@ "Data and Functions from the book R Graphics, Second Edition. There is a function to produce each figure in the book, plus several functions, classes, and methods defined in Chapter 8.") (license license:gpl2+))) -(define-public pylmm-gn2 - (let ((commit "3c6d1cac8")) - (package - (name "pylmm-gn2") - (version (string-append "1.0-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/genenetwork/pylmm.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964")))) - (build-system python-build-system) - (inputs `( - ("python2-setuptools" ,python2-setuptools) - ("python2-scipy" ,python2-scipy) - ("python2-numpy" ,python2-numpy) - )) - (arguments - `(#:python ,python-2 - #:tests? #f ; no 'setup.py test' - #:phases - (modify-phases %standard-phases - (add-before - 'build 'change-paths - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* "scripts/pylmm_redis" - (("/usr/bin/python") (which "python")) - (("\\$PACKAGEDIR") (string-append out "/lib/python2.7/site-packages"))) - )))))) - - (home-page "http://genenetwork.org/") - (synopsis "LMM resolver") - (description "Fast and lightweight linear mixed-model (LMM) solver -for use in genome-wide association studies (GWAS).") - (license license:agpl3+)))) - (define-public r-ctl ; guix: ready (package (name "r-ctl") |