diff options
Diffstat (limited to 'guix.scm')
| -rw-r--r-- | guix.scm | 97 |
1 files changed, 35 insertions, 62 deletions
diff --git a/guix.scm b/guix.scm index 9b8f399..9bf23c8 100644 --- a/guix.scm +++ b/guix.scm @@ -17,72 +17,47 @@ ;;; 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 - (srfi srfi-1) - (srfi srfi-26) - (ice-9 match) - (ice-9 popen) - (ice-9 rdelim) - (gn packages gemma) - (gn packages python) - (gnu packages base) - (gnu packages check) - (gnu packages graph) - (gnu packages cran) - (gnu packages databases) - (gnu packages statistics) - (gnu packages bioconductor) - (gnu packages golang) - (gn packages genenetwork) - (gnu packages python) - (gnu packages python-check) - (gnu packages python-crypto) - (gnu packages python-web) - (gnu packages python-xyz) - (gnu packages python-science) - ((guix build utils) #:select (with-directory-excursion)) - (guix build-system python) - (guix gexp) - (guix git-download) - (guix licenses) - (guix packages)) +(use-modules (gn packages gemma) + (gn packages python) + (gnu packages base) + (gnu packages check) + (gnu packages graph) + (gnu packages cran) + (gnu packages databases) + (gnu packages statistics) + (gnu packages bioconductor) + (gnu packages golang) + (gn packages genenetwork) + (gnu packages python) + (gnu packages python-check) + (gnu packages python-crypto) + (gnu packages python-web) + (gnu packages python-xyz) + (gnu packages python-science) + ((guix build utils) #:select (with-directory-excursion)) + (guix build-system python) + (guix gexp) + (guix git-download) + (guix licenses) + (guix packages)) (define %source-dir (dirname (current-filename))) -(define git-file? - (let* ((pipe (with-directory-excursion %source-dir - (open-pipe* OPEN_READ "git" "ls-files"))) - (files (let loop ((lines '())) - (match (read-line pipe) - ((? eof-object?) - (reverse lines)) - (line - (loop (cons line lines)))))) - (status (close-pipe pipe))) - (lambda (file stat) - (match (stat:type stat) - ('directory #t) - ((or 'regular 'symlink) - (any (cut string-suffix? <> file) files)) - (_ #f))))) (package (name "genenetwork3.git") - (version "0.0.1") - (source (local-file %source-dir + (version "0.1.0") + (source (local-file %source-dir "genenetwork3-checkout" #:recursive? #t - #:select? git-file?)) + #:select? (git-predicate %source-dir))) (propagated-inputs `(("coreutils" ,coreutils) ("gemma-wrapper" ,gemma-wrapper) ("gunicorn" ,gunicorn) @@ -90,27 +65,25 @@ ("python-bcrypt" ,python-bcrypt) ("python-flask" ,python-flask) ("python-flask-cors" ,python-flask-cors) + ("python-flask-socketio" ,python-flask-socketio) ("python-ipfshttpclient" ,python-ipfshttpclient) ("python-mypy" ,python-mypy) ("python-mypy-extensions" ,python-mypy-extensions) ("python-mysqlclient" ,python-mysqlclient) ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pingouin" ,python-pingouin) ("python-plotly" ,python-plotly) ("python-pylint" ,python-pylint) ("python-redis" ,python-redis) ("python-requests" ,python-requests) ("python-scipy" ,python-scipy) - ("python-sqlalchemy-stubs" - ,python-sqlalchemy-stubs) ("r-optparse" ,r-optparse) ("r-qtl" ,r-qtl) + ("r-rjson" ,r-rjson) ("r-stringi" ,r-stringi) ("r-wgcna" ,r-wgcna) - ("r-rjson" ,r-rjson) - ("python-plotly" ,python-plotly) - ("python-pandas" ,python-pandas) - ("rust-qtlreaper" ,rust-qtlreaper) - ("python-flask-cors" ,python-flask-cors))) + ("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.") |