diff options
| -rw-r--r-- | gn/packages/gemma.scm | 28 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 30 | ||||
| -rw-r--r-- | gn/packages/shell.scm | 12 |
3 files changed, 62 insertions, 8 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm index 3c40317..9986bf5 100644 --- a/gn/packages/gemma.scm +++ b/gn/packages/gemma.scm @@ -63,28 +63,42 @@ #:use-module (srfi srfi-1)) (define-public gemma-git ; guix candidate - (let ((commit "5675bdf0422f63f81752bb1fcf7b436bc30bf9b7")) + (let ((commit "c978835c3630286414df6076d38aad16277cdb6b")) (package (name "gemma-git") - (version (string-append "0.95.2a" commit )) + (version (string-append "0.97-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/xiangzhou/GEMMA") + (url "https://github.com/genenetwork/GEMMA") (commit commit))) (file-name (string-append name "-" commit)) (sha256 (base32 - "0qc8dx8m4cqggnin2vsbc9l91ay6h04l0mpjv8z0wcickqb4lby6")))) + "1hw8y7vka79v84lv5vyhkinx864yjh1wd8vfd16cvqs1bi8qw3n2")))) (inputs `( ("gsl" ,gsl) + ("eigen" ,eigen) ("lapack" ,lapack) + ("openblas" ,openblas) ("zlib" ,zlib) )) + (native-inputs ; for running tests + `(("shunit2" ,shunit2) + ("which" ,which) + )) + (build-system gnu-build-system) (arguments - `(#:make-flags '(" FORCE_DYNAMIC=1") + `(#:make-flags + (list + (string-append "EIGEN_INCLUDE_PATH=" + (assoc-ref %build-inputs "eigen") + "/include/eigen3/") + "FORCE_DYNAMIC=1" + "WITH_OPENBLAS=1") #:phases + ; "/include/eigen3/" (modify-phases %standard-phases (delete 'configure) (add-before 'build 'bin-mkdir @@ -95,8 +109,8 @@ (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (install-file "bin/gemma" (string-append out "/bin")))))) - #:tests? #f)) - (home-page "") + #:parallel-tests? #f)) + (home-page "http://www.xzlab.org/software.html") (synopsis "Tool for genome-wide efficient mixed model association") (description "GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 08a8954..34178b5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -91,7 +91,32 @@ (description #f) (license #f))) -(define-public qtlreaper ; guix obsolete - but used in GN2 +(define-public qn-server ; guix obsolete - but used in GN2 + (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) + (package + (name "qn-server") + (version (string-append "1.1-gn2-" (string-take commit 7) )) + (source (origin + (method git-fetch) + (uri (git-reference + ;; (url "https://github.com/genenetwork/genenetwork2.git") + (url "https://github.com/pjotrp/QTLreaper.git") + (commit commit))) + (file-name (string-append name "-" (string-take commit 7))) + (sha256 + (base32 + "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; no 'setup.py test' really! + (home-page "") + (synopsis "GeneNetwork REST API") + (description +"") + (license license:gpl2+)))) + +(define-public qtlreaper (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) (package (name "qtlreaper") @@ -143,6 +168,7 @@ location of a putative QTL.") ("python" ,python-2) ;; probably superfluous ("git" ,git) ("which" ,which) + ("grep" ,grep) ("r" ,r) ("r-ctl" ,r-ctl) ("r-phewas" ,r-phewas) @@ -198,6 +224,8 @@ location of a putative QTL.") (("echo") (which "echo")) (("redis-server") (which "redis-server")) (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) (("which") (which "which")) ; three wiches in a row! )#t)) (add-before 'install 'fix-paths diff --git a/gn/packages/shell.scm b/gn/packages/shell.scm index e457dce..eb9178f 100644 --- a/gn/packages/shell.scm +++ b/gn/packages/shell.scm @@ -3,6 +3,7 @@ #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (gnu packages) + #:use-module (gnu packages base) #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) ) @@ -20,6 +21,9 @@ (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "11savxc6qliqv25kv59qak6j7syjv95hbpmq1szn1mzn32g2gc25")))) + (inputs `( + ("coreutils" ,coreutils) ; for mktemp and od + )) (build-system gnu-build-system) (arguments `( @@ -28,6 +32,14 @@ (modify-phases %standard-phases (delete 'configure) (delete 'build) + (add-after 'unpack 'replace-binary-paths + (lambda _ + (substitute* "source/2.0/src/shell/shunit2" + (("/bin/sh") (which "sh")) + (("exec mktemp") (string-append "exec " (which "mktemp"))) + (("/usr/bin/od") (which "od")) + )#t)) + (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) |