diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 41 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 6 |
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" )) ) )))) |