diff options
| -rw-r--r-- | README.md | 18 | ||||
| -rw-r--r-- | guix.scm | 11 |
2 files changed, 26 insertions, 3 deletions
@@ -11,7 +11,7 @@ Simply load up the environment (for development purposes): guix environment --load=guix.scm ``` -Also, make sure you have the *guix-bioinformatics* channel set up. +Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm @@ -22,9 +22,21 @@ python3 Better run a proper container ``` -env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm +env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm ``` +If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception: +error: python-sqlalchemy-stubs: unbound variable` it typically means an update to guix latest is required (i.e., guix pull): + +``` +guix pull +source ~/.config/guix/current/etc/profile +``` + +and try again. + +See also instructions in [.guix.scm](.guix.scm). + #### Running Tests (assuming you are in a guix container; otherwise use venv!) @@ -71,7 +83,7 @@ virtualenv --python python3 venv ```bash # The --ignore-installed flag forces packages to -# get installed in the venv even if they existed +# get installed in the venv even if they existed # in the global env pip install -r requirements.txt --ignore-installed ``` @@ -17,6 +17,17 @@ ;;; 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 +;; +;; To get a development container (e.g., run in emacs shell). +;; +;; env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm + (use-modules (srfi srfi-1) (srfi srfi-26) |