diff options
| -rw-r--r-- | README.md | 10 | ||||
| -rw-r--r-- | gn3/settings.py | 1 | ||||
| -rw-r--r-- | guix.scm | 22 | ||||
| -rw-r--r-- | setup.py | 1 |
4 files changed, 13 insertions, 21 deletions
diff --git a/README.md b/README.md index 84e5fb9..62e8aeb 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,8 @@ Install GNU Guix - this can be done on every running Linux system. There are at least three ways to start GeneNetwork3 with GNU Guix: -1. Create an environment with `guix environment` -2. Create a container with `guix environment -C` +1. Create an environment with `guix shell` +2. Create a container with `guix shell -C` 3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile` #### Create an environment: @@ -18,13 +18,13 @@ There are at least three ways to start GeneNetwork3 with GNU Guix: Simply load up the environment (for development purposes): ```bash -guix environment --load=guix.scm +guix shell -Df guix.scm ``` Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash -guix environment --expose=$HOME/genotype_files/ --load=guix.scm +guix shell --expose=$HOME/genotype_files/ -Df guix.scm python3 import redis ``` @@ -32,7 +32,7 @@ python3 #### Run a Guix container ``` -guix environment -C --network --expose=$HOME/genotype_files/ --load=guix.scm +guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm ``` diff --git a/gn3/settings.py b/gn3/settings.py index eaf8f23..0ac6698 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -17,7 +17,6 @@ RQTL_WRAPPER = "rqtl_wrapper.R" SQL_URI = os.environ.get( "SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") SECRET_KEY = "password" -SQLALCHEMY_TRACK_MODIFICATIONS = False # gn2 results only used in fetching dataset info GN2_BASE_URL = "http://www.genenetwork.org/" diff --git a/guix.scm b/guix.scm index a48b05a..9bf23c8 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) @@ -68,27 +65,24 @@ ("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-flask-socketio" ,python-flask-socketio) - ("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) - ("python-pingouin" ,python-pingouin) ("rust-qtlreaper" ,rust-qtlreaper))) (build-system python-build-system) (home-page "https://github.com/genenetwork/genenetwork3") diff --git a/setup.py b/setup.py index 98a076f..55b4be2 100644 --- a/setup.py +++ b/setup.py @@ -19,7 +19,6 @@ setup(author='Bonface M. K.', "redis==3.5.3" "requests==2.25.1" "scipy==1.6.0" - "sqlalchemy-stubs==0.4" "plotly==4.14.3" "flask-cors==3.0.9" ], |