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-rw-r--r--gn/packages/bioinformatics.scm41
-rw-r--r--gn/packages/genenetwork.scm6
2 files changed, 24 insertions, 23 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c04c6c8..f62949d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -830,7 +830,7 @@ confidence region for the location of a putative QTL.")
(replace 'build
(lambda _
(zero? (system* "make" "-f" "Makefile.std"))
- ))
+ ))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
@@ -861,45 +861,46 @@ subsequent visualization, annotation and storage of results.")
(license (list license:gpl2 license:lgpl2.1+))))
(define-public plink-ng
- (let ((commit "6ab6ecf81e904b7db76454422ea59baae437d961"))
+ (let ((commit "5d1db4313ba0cc976562da233db4aced78975d10"))
(package
(name "plink-ng")
- (version (string-append "1.90b3-" commit ))
+ (version (string-append "1.90b3-" commit )) ; Aug 11, 2016
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/chrchang/plink-ng.git")
+ (url "https://github.com/genenetwork/plink-ng.git")
(commit commit)))
- (file-name (string-append name "-" commit))
+ (file-name (string-append name "-" commit))
(sha256
(base32
- "0djnfcr3lm6839lkglpq1p4w09zlgv68p618c2i5dng4jhwji94k"))))
- ;;; (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch"))
+ "1366li3ks9076bblvd1rpzkjq4j8f8f08lhga4c1ckrkil3xww4m"))))
+ ;; no longer (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("openblas" ,openblas)
+ ;; ("atlas" ,atlas) ; openblas replaces atlas
+ ("lapack" ,lapack) ; lapack is disabled in GUIX openblas
+ ;; ("gfortran" ,gfortran)
+ ;; ("python" ,python-2) ;; for tests - currently disabled
+ ))
+ (native-inputs
+ `(("unzip" ,unzip)))
(build-system gnu-build-system)
(arguments
- '(#:tests? #f ;no "check" target
+ '(#:tests? #f ;no "check" target. Some of the python-based tests fail
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
- (zero? (system* "make" "-f" "Makefile.std"))
- ))
+ (zero? (system* "make" "-f" "Makefile.guix"))
+ ))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin/")))
(install-file "plink2" bin)
#t))))))
- (inputs
- `(("zlib" ,zlib)
- ("openblas" ,openblas)
- ;; ("atlas" ,atlas)
- ;; ("lapack" ,lapack)
- ("gfortran" ,gfortran)
- ))
- (native-inputs
- `(("unzip" ,unzip)))
(home-page "https://www.cog-genomics.org/plink2")
(synopsis "Whole genome association analysis toolset")
(description
@@ -922,7 +923,7 @@ subsequent visualization, annotation and storage of results.")
(uri (git-reference
(url "https://github.com/genenetwork/GEMMA.git")
(commit commit)))
- (file-name (string-append name "-" commit))
+ (file-name (string-append name "-" commit))
(sha256
(base32
"1drffdgwbzgiw9sf55ghl3zjv58f8i9kfz0zys5mp6n06syp4ira"))))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 81873d5..a7317c6 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -163,8 +163,8 @@
("mysql" ,mysql)
("gemma" ,gemma-git)
("genenetwork2-files-small" ,genenetwork2-files-small)
+ ("plink-ng" ,plink-ng)
("pylmm-gn2" ,pylmm-gn2)
- ;; ("plink2" ,plink-ng) disabled - FIXME
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("python2-htmlgen-gn" ,python2-htmlgen-gn)
@@ -200,14 +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 "plink-ng") "/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" ))
)
))))