Add a systemd unit for running the pipeline and use conda run

PavlidisLab · May 23, 2024 · fb399fa · fb399fa
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diff --git a/data/rnaseq-pipeline-viewer.service b/data/rnaseq-pipeline-viewer.service
diff --git a/data/systemd/README.md b/data/systemd/README.md
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+This directory contains systemctl unit and timers to launch the RNA-Seq
+pipeline and its webviewer.
+
diff --git a/data/systemd/rnaseq-pipeline-viewer.service b/data/systemd/rnaseq-pipeline-viewer.service
@@ -0,0 +1,13 @@
+[Unit]
+Description=PavLab RNA-Seq Pipeline Viewer
+Requires=luigid.service
+After=multi-user.target
+
+[Service]
+Type=simple
+WorkingDirectory=/space/grp/Pipelines/rnaseq-pipeline
+ExecStart=/space/grp/poirigui/miniconda3/condabin/conda run --no-capture-output -p /space/grp/Pipelines/rnaseq-pipeline/env gunicorn -e SCRIPT_NAME=/rnaseq-pipeline -b 0.0.0.0:8000 rnaseq_pipeline.webviewer:app --access-logfile pipeline-output/webviewer-logs/access.log --error-logfile pipeline-output/webviewer-logs/error.log
+User=poirigui
+
+[Install]
+WantedBy=multi-user.target
diff --git a/data/systemd/rnaseq-pipeline.service b/data/systemd/rnaseq-pipeline.service
@@ -0,0 +1,13 @@
+[Unit]
+Description=PavLab RNA-Seq Pipeline
+Requires=luigid.service
+After=multi-user.target
+
+[Service]
+Type=simple
+WorkingDirectory=/space/grp/Pipelines/rnaseq-pipeline
+ExecStart=/space/grp/poirigui/miniconda3/condabin/conda run --no-capture-output -p /space/grp/Pipelines/rnaseq-pipeline/env submit-experiments-from-gsheet --spreadsheet-id 17xm2eFFqhhT-M6-jTC_lsar7RMgk8Ln-TwQPDWlRfIY --sheet-name RNA-SEQ --workers 200
+User=poirigui
+
+[Install]
+WantedBy=multi-user.target