Update systemd units

Author: arteymix

Makefile

@@ -26,7 +26,7 @@ install-python:
 
 install-systemd-units:
 	mkdir -p "${DESTDIR}/etc/systemd/system/"
-	install data/systemd/rnaseq-pipeline-viewer.service data/systemd/[email protected] "${DESTDIR}/etc/systemd/system/"
+	install data/systemd/*.{service,timer,target} "${DESTDIR}/etc/systemd/system/"
 	@echo "Remember to run 'systemctl override rnaseq-pipeline-viewer' and 'systemctl override rnaseq-pipeline-worker@' and set CONDA_BIN, CONDA_ENV, GEMMA_USERNAME and GEMMA_PASSWORD environment variables."
 
 install-RSEM:

data/systemd/README.md

@@ -1,3 +1,43 @@
 This directory contains systemctl unit and timers to launch the RNA-Seq
 pipeline and its webviewer.
 
+To edit the configuration, issue: `systemctl edit [email protected]` and `systemctl edit rnaseq-pipeline-viewer.service`
+to add the following environment variables:
+
+```
+[Service]
+WorkingDirectory=/location/of/the/pipeline/configuration
+Environment="CONDA_ENV=/path/to/conda/env"
+Environment="GEMMA_USERNAME={username}"
+Environment="GEMMA_PASSWORD={password}"
+```
+
+# Launch workers
+
+We run two workers, one is generally idle and awaits new datasets to be
+processed in a collaborative spreadsheet by our curators, the other is
+generally busy. Those are configured to restart after 20 minutes after exiting.
+
+```
+systemctl start [email protected] [email protected]
+```
+
+# Launch the viewer
+
+```
+systemctl start rnaseq-pipeline-viewer.service
+```
+
+# Enable the cleanup unit
+
+Edit the configuration to set the working directory where the cleanup script
+can be resolved.
+
+```
+[Service]
+WorkingDirectory=/location/of/the/pipeline/configuration
+```
+
+```
+systemctl start rnaseq-pipeline-cleanup.timer
+```

data/systemd/rnaseq-pipeline-cleanup.service

@@ -0,0 +1,6 @@
+[Unit]
+Description=PavLab RNA-Seq Pipeline Cleanup
+
+[Service]
+Type=simple
+ExecStart=/bin/bash -c "./scripts/remove-old-data"

data/systemd/rnaseq-pipeline-cleanup.timer

@@ -0,0 +1,8 @@
+[Unit]
+Description=Cleanup the RNA-Seq Pipeline hourly
+
+[Timer]
+OnCalendar=hourly
+
+[Install]
+WantedBy=timers.target

data/systemd/rnaseq-pipeline-viewer.service

@@ -1,13 +1,11 @@
 [Unit]
 Description=PavLab RNA-Seq Pipeline Viewer
 Requires=luigid.service
-After=multi-user.target
+After=network.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
+ExecStart=/bin/bash -c "conda run --no-capture-output -p $CONDA_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"
 
 [Install]
 WantedBy=multi-user.target

data/systemd/[email protected]

@@ -0,0 +1,8 @@
+[Unit]
+Description=PavLab RNA-Seq Pipeline Worker #%i
+Requires=luigid.service
+After=network.target
+
+[Service]
+Type=simple
+ExecStart=bash -c "conda run --no-capture-output -p $CONDA_ENV luigi-wrapper --module rnaseq_pipeline.tasks --assistant --workers 200"

data/systemd/rnaseq-pipeline.service

@@ -0,0 +1,6 @@
+#!/bin/sh
+
+output_dir=/cosmos/data/pipeline-output/rnaseq
+
+find "$output_dir/data/sra" -mtime +30 -delete -print
+find "$output_dir/data-trimmed" -mtime +30 -delete -print