From 570d7b6118739bb76b6d32881e9ef45e50a9e3ae Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 4 Mar 2016 13:29:23 +0000 Subject: python-mysqlclient: propagate the shared lib --- gn/packages/python.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gn/packages/python.scm') diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 7781521..6fff9a3 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -279,16 +279,14 @@ powerful language for representing information.") (base32 "06qzgwk7j66k8ggx51i6wxx0f0zsppp7w4bh6gjd0cr9rfs86jn7")))) (build-system python-build-system) - (inputs + (propagated-inputs `( ("mysql" ,mysql) ("python-nose" ,python-nose) ("zlib" ,zlib) ("openssl" ,openssl) ("libgcrypt" ,libgcrypt) - )) - (propagated-inputs - `(("python-setuptools" ,python-setuptools) + ("python-setuptools" ,python-setuptools) )) (arguments `(#:tests? #f)) ; wants a running MySQL server -- cgit v1.2.3 From a4a9f2eec7a770a52bbeda64169ba9e3b1ff2583 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sat, 5 Mar 2016 16:07:32 +0000 Subject: Guix paths to the tools --- gn/packages/bioinformatics.scm | 2 +- gn/packages/genenetwork.scm | 20 +++++++++++++++++--- gn/packages/python.scm | 2 ++ 3 files changed, 20 insertions(+), 4 deletions(-) (limited to 'gn/packages/python.scm') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 295a2b3..c04c928 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -305,8 +305,8 @@ length of a short-read sequencing alignment.") (propagated-inputs `( ;; ("r-annotationdbi" ,r-annotationdbi) ; ("r-biocparallel" ,r-biocparallel) - ("r-dynamictreecut" ,r-dynamictreecut) ("r-doparallel" ,r-doparallel) + ("r-dynamictreecut" ,r-dynamictreecut) ("r-fastcluster" ,r-fastcluster) ("r-foreach" ,r-foreach) ("r-go-db" ,r-go-db) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index fdcbb7f..c952792 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -154,10 +154,14 @@ (sha256 (base32 "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) + (inputs `( + ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) @@ -190,7 +194,6 @@ ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) )) (build-system python-build-system) (arguments @@ -199,9 +202,20 @@ (modify-phases %standard-phases (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) - (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))) + (let* ( + (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) + (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + ) + (substitute* '("etc/default_settings.py") - (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))))))) + (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\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" )) + ) + )))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 6fff9a3..8157c0b 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -432,6 +432,8 @@ version ".tgz")) (build-system python-build-system) (native-inputs `(("python2-setuptools" ,python2-setuptools))) + (propagated-inputs + `(("python2-pil" ,python2-pil))) (arguments `( #:python ,python-2 -- cgit v1.2.3 From f6832be1fe9138418bdd2858dbb2fc305cbcb25e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 9 Mar 2016 11:34:55 -0500 Subject: Small fixed --- gn/packages/bioinformatics.scm | 1 + gn/packages/python.scm | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) (limited to 'gn/packages/python.scm') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 5bf7843..e6aa90f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -22,6 +22,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages cmake) #:use-module (gnu packages cpio) + #:use-module (gnu packages cppcheck) #:use-module (gnu packages file) #:use-module (gnu packages gcc) #:use-module (gnu packages graphviz) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 8157c0b..47b2c23 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -355,7 +355,7 @@ project)") (description #f) (license #f))) -(define-public python2-pil-1.1.6 +(define-public python2-pil (package (name "python2-pil") (version "1.1.6") -- cgit v1.2.3