diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 2 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 20 | ||||
| -rw-r--r-- | gn/packages/python.scm | 2 |
3 files changed, 20 insertions, 4 deletions
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 |