Use environment conda to run integration

.gitlab-ci.yml

@@ -9,11 +9,11 @@ variables:
 
 .singularity_before_script_anchor: &singularity_before_script_anchor
   before_script:
-    - pip install -r requirements.txt
-    - pip install -r requirements-dev.txt
     - export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
+    - source ${CONDA_SH}
+    - conda activate hutspot-pipeline
+    - export PATH=${PATH}:${SINGULARITY_PATH}
     - echo $BASETEMP
-    - mkdir -p $BASETEMP
 
 stages:
   - sanity
@@ -42,7 +42,7 @@ test_dry_run:
 test_integration:
   <<: *singularity_before_script_anchor
   script:
-    - pytest-3 --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
+    - pytest --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
   tags:
     - slurm
   stage: integration