From 12a30bd92d854ecf5b8736758d142dcdb534afec Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Fri, 15 May 2020 08:57:03 +0200
Subject: [PATCH] Add vcf-to-varda conda env
---
.gitlab-ci.yml | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 435316b..bf2653c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,6 +5,14 @@ variables:
before_script:
- pip3 install pytest-workflow
+.slurm_before_script_anchor: &slurm_before_script_anchor
+ before_script:
+ - export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
+ - source ${CONDA_SH}
+ - conda activate vcf-to-varda
+ - export PATH=${PATH}:${SINGULARITY_PATH}
+ - echo $BASETEMP
+
stages:
- sanity
- dry-run
@@ -19,9 +27,9 @@ test-sanity:
stage: sanity
test-dry-run:
- <<: *before_script_anchor
+ <<: *slurm_before_script_anchor
script:
- - pytest --keep-workflow-wd-on-fail --tag dry-run
+ - pytest --keep-workflow-wd-on-fail --basetemp ${BASETEMP} --tag dry-run
image: lumc/singularity-snakemake:3.5.2-5.15.0
tags:
- slurm
--
GitLab