diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 87 |
1 files changed, 38 insertions, 49 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 70eb13016a..0030969d8d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -139,6 +139,7 @@ #:use-module (gnu packages qt) #:use-module (gnu packages rdf) #:use-module (gnu packages readline) + #:use-module (gnu packages rpc) #:use-module (gnu packages rsync) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) @@ -6233,67 +6234,55 @@ distribution, coverage uniformity, strand specificity, etc.") (license license:gpl3+))) (define-public seek - ;; There are no release tarballs. According to the installation - ;; instructions at http://seek.princeton.edu/installation.jsp, the latest - ;; stable release is identified by this changeset ID. - (let ((changeset "2329130") + ;; There are no release tarballs. And the installation instructions at + ;; http://seek.princeton.edu/installation.jsp only mention a mercurial + ;; changeset ID. This is a git repository, though. So we just take the + ;; most recent commit. + (let ((commit "196ed4c7633246e9c628e4330d77577ccfd7f1e5") (revision "1")) (package (name "seek") - (version (string-append "0-" revision "." changeset)) + (version (git-version "1" revision commit)) (source (origin - (method hg-fetch) - (uri (hg-reference - (url "https://bitbucket.org/libsleipnir/sleipnir") - (changeset changeset))) - (file-name (string-append name "-" version "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/FunctionLab/sleipnir.git") + (commit commit) + (recursive? #true))) + (file-name (git-file-name name version)) (sha256 (base32 - "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) - (build-system gnu-build-system) + "0c658n8nz563a96dsi4gl2685vxph0yfmmqq5yjc6i4xin1jy1ab")))) + (build-system cmake-build-system) (arguments - `(#:modules ((srfi srfi-1) - (guix build gnu-build-system) - (guix build utils)) + `(#:configure-flags + ,#~(list (string-append "-DSVM_LIBRARY=" + #$(this-package-input "libsvm") + "/lib/libsvm.so.2") + (string-append "-DSVM_INCLUDE=" + #$(this-package-input "libsvm") + "/include")) + #:tests? #false ; tests only fail in the build container #:phases - (let ((dirs '("SeekMiner" - "SeekEvaluator" - "SeekPrep" - "Distancer" - "Data2DB" - "PCL2Bin"))) - (modify-phases %standard-phases - (replace 'bootstrap - (lambda _ - (substitute* "gen_tools_am" - (("/usr/bin/env.*") (which "perl"))) - (invoke "bash" "gen_auto") - #t)) - (add-after 'build 'build-additional-tools - (lambda* (#:key make-flags #:allow-other-keys) - (for-each (lambda (dir) - (with-directory-excursion (string-append "tools/" dir) - (apply invoke "make" make-flags))) - dirs) - #t)) - (add-after 'install 'install-additional-tools - (lambda* (#:key make-flags #:allow-other-keys) - (for-each (lambda (dir) - (with-directory-excursion (string-append "tools/" dir) - (apply invoke `("make" ,@make-flags "install")))) - dirs) - #t)))))) + (modify-phases %standard-phases + ;; The check phase expects to find the unit_tests executable in the + ;; "build/bin" directory, but it is actually in "build/tests". + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "tests/unit_tests"))))))) (inputs - `(("gsl" ,gsl) + `(("apache-thrift:include" ,apache-thrift "include") + ("apache-thrift:lib" ,apache-thrift "lib") + ("gsl" ,gsl) ("boost" ,boost) - ("libsvm" ,libsvm) - ("readline" ,readline) ("gengetopt" ,gengetopt) - ("log4cpp" ,log4cpp))) + ("libsvm" ,libsvm) + ("log4cpp" ,log4cpp) + ("python" ,python) + ("readline" ,readline))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("perl" ,perl))) + `(("pkg-config" ,pkg-config))) (home-page "http://seek.princeton.edu") (synopsis "Gene co-expression search engine") (description |