diff options
Diffstat (limited to 'guix.scm')
| -rw-r--r-- | guix.scm | 52 |
1 files changed, 7 insertions, 45 deletions
diff --git a/guix.scm b/guix.scm index a48b05a..943c80e 100644 --- a/guix.scm +++ b/guix.scm @@ -17,16 +17,13 @@ ;;; You should have received a copy of the GNU General Public License ;;; along with genenetwork3. If not, see https://www.gnu.org/licenses/. -;; To use this file to build HEAD of gemma: -;; -;; env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix build -f guix.scm -;; -;; After checking out the git repo -;; cd ~ ; git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics +;; Make sure you have the +;; https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics channel +;; set up. ;; ;; To get a development container (e.g., run in emacs shell). ;; -;; env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm +;; guix shell -C -Df guix.scm (use-modules (gn packages gemma) (gn packages python) @@ -45,6 +42,7 @@ (gnu packages python-web) (gnu packages python-xyz) (gnu packages python-science) + (gnu packages rdf) ((guix build utils) #:select (with-directory-excursion)) (guix build-system python) (guix gexp) @@ -54,44 +52,8 @@ (define %source-dir (dirname (current-filename))) - (package - (name "genenetwork3.git") - (version "0.1.0") + (inherit genenetwork3) (source (local-file %source-dir "genenetwork3-checkout" #:recursive? #t - #:select? (git-predicate %source-dir))) - (propagated-inputs `(("coreutils" ,coreutils) - ("gemma-wrapper" ,gemma-wrapper) - ("gunicorn" ,gunicorn) - ("python" ,python-wrapper) - ("python-bcrypt" ,python-bcrypt) - ("python-flask" ,python-flask) - ("python-flask-cors" ,python-flask-cors) - ("python-ipfshttpclient" ,python-ipfshttpclient) - ("python-mypy" ,python-mypy) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-mysqlclient" ,python-mysqlclient) - ("python-numpy" ,python-numpy) - ("python-plotly" ,python-plotly) - ("python-pylint" ,python-pylint) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-scipy" ,python-scipy) - ("python-flask-socketio" ,python-flask-socketio) - ("python-sqlalchemy-stubs" - ,python-sqlalchemy-stubs) - ("r-optparse" ,r-optparse) - ("r-qtl" ,r-qtl) - ("r-stringi" ,r-stringi) - ("r-wgcna" ,r-wgcna) - ("r-rjson" ,r-rjson) - ("python-plotly" ,python-plotly) - ("python-pandas" ,python-pandas) - ("python-pingouin" ,python-pingouin) - ("rust-qtlreaper" ,rust-qtlreaper))) - (build-system python-build-system) - (home-page "https://github.com/genenetwork/genenetwork3") - (synopsis "GeneNetwork3 API for data science and machine learning.") - (description "GeneNetwork3 API for data science and machine learning.") - (license agpl3+)) + #:select? (git-predicate %source-dir)))) |