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authorPjotr Prins2016-08-14 02:16:30 -0500
committerPjotr Prins2016-08-14 02:16:30 -0500
commitb3394e07071d11674cc796e6a4a3de5fc4634a78 (patch)
treea5b582c13e1c8ac796a7fc0ac8bca3a6672e1981 /gn
parent71fd1cbbd9fb97b6893f707123f843a9d9ab7522 (diff)
downloadguix-bioinformatics-b3394e07071d11674cc796e6a4a3de5fc4634a78.tar.gz
Getting GN2 ready for new build - plink-ng is disabled and should not be built with atlas and lapack (FIXME)
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm14
-rw-r--r--gn/packages/genenetwork.scm9
2 files changed, 10 insertions, 13 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c1b22fd..c04c6c8 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -840,8 +840,8 @@ confidence region for the location of a putative QTL.")
(inputs
`(("zlib" ,zlib)
("openblas" ,openblas)
- ("atlas" ,atlas)
- ("lapack" ,lapack)
+ ;; ("atlas" ,atlas)
+ ;; ("lapack" ,lapack)
("gfortran" ,gfortran)
))
(native-inputs
@@ -861,7 +861,7 @@ subsequent visualization, annotation and storage of results.")
(license (list license:gpl2 license:lgpl2.1+))))
(define-public plink-ng
- (let ((commit "516d730f9"))
+ (let ((commit "6ab6ecf81e904b7db76454422ea59baae437d961"))
(package
(name "plink-ng")
(version (string-append "1.90b3-" commit ))
@@ -873,8 +873,8 @@ subsequent visualization, annotation and storage of results.")
(file-name (string-append name "-" commit))
(sha256
(base32
- "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf580"))
- (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
+ "0djnfcr3lm6839lkglpq1p4w09zlgv68p618c2i5dng4jhwji94k"))))
+ ;;; (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch"))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
@@ -894,8 +894,8 @@ subsequent visualization, annotation and storage of results.")
(inputs
`(("zlib" ,zlib)
("openblas" ,openblas)
- ("atlas" ,atlas)
- ("lapack" ,lapack)
+ ;; ("atlas" ,atlas)
+ ;; ("lapack" ,lapack)
("gfortran" ,gfortran)
))
(native-inputs
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 4f3d356..10f0a26 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -164,7 +164,7 @@
("gemma" ,gemma-git)
("genenetwork2-files-small" ,genenetwork2-files-small)
("pylmm-gn2" ,pylmm-gn2)
- ("plink2" ,plink-ng)
+ ;; ("plink2" ,plink-ng) disabled - FIXME
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("python2-htmlgen-gn" ,python2-htmlgen-gn)
@@ -173,7 +173,6 @@
("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
("python2-setuptools" ,python2-setuptools)
("python2-scipy" ,python2-scipy)
- ;; looks like python-numarray is not needed
("python2-mysqlclient" ,python2-mysqlclient)
("python2-numarray" ,python2-numarray)
("python2-numpy" ,python2-numpy)
@@ -189,8 +188,6 @@
("python2-simplejson" ,python2-simplejson)
("python2-pyyaml" ,python2-pyyaml)
("python2-xlsxwriter" ,python2-xlsxwriter)
- ;; python-yolk is not needed
- ("plink" ,plink)
("qtlreaper" ,qtlreaper)
))
(build-system python-build-system)
@@ -203,14 +200,14 @@
(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"))
+ ;; (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" ))
(("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
- (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
+ ;; (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
)
))))