fix for hpc jobs

dags/dag1_calculate_hpc_worker.py

@@ -96,9 +96,9 @@ with dag:
       queue='igf-lims',
       command="""
       {% if ti.xcom_pull(key=params.job_name,task_ids="calculate_new_worker_size_and_branch" ) > 1 %}
-        echo "qsub -V -N {{ params.job_name }} -J 1-{{ ti.xcom_pull(key=params.job_name,task_ids="calculate_new_worker_size_and_branch" ) }}  {{ params.pbs_resource }} -- /project/tgu/data2/airflow_test/github/igf-airflow-hpc/scripts/hpc/airflow_worker.sh {{  params.airflow_queue }} {{ params.job_name }}"
+        source /etc/bashrc;qsub -N {{ params.job_name }} -J 1-{{ ti.xcom_pull(key=params.job_name,task_ids="calculate_new_worker_size_and_branch" ) }}  {{ params.pbs_resource }} -- /project/tgu/data2/airflow_test/github/igf-airflow-hpc/scripts/hpc/airflow_worker.sh {{  params.airflow_queue }} {{ params.job_name }}
       {% else %}
-        echo "qsub -V -N {{ params.job_name }} {{ params.pbs_resource }} -- /project/tgu/data2/airflow_test/github/igf-airflow-hpc/scripts/hpc/airflow_worker.sh {{  params.airflow_queue }} {{ params.job_name }}"
+        source /etc/bashrc;qsub -N {{ params.job_name }} {{ params.pbs_resource }} -- /project/tgu/data2/airflow_test/github/igf-airflow-hpc/scripts/hpc/airflow_worker.sh {{  params.airflow_queue }} {{ params.job_name }}
       {% endif %}
       """,
       params={'pbs_resource':pbs_resource,'airflow_queue':airflow_queue,'job_name':q}

scripts/hpc/hpc_env_template.sh

@@ -1,5 +1,3 @@
-source /etc/bashrc;
-
 module load anaconda3/personal
 source activate airflow1.10.12