Merge pull request #72 from johandahlberg/bcl2fastq_path_configurable

Make the bcl2fastq binary path configurable

ansible-st2-local/roles/bcl2fastq/defaults/main.yml

@@ -7,6 +7,9 @@ arteria_bcl2fastq_app_config: "{{ arteria_bcl2fastq_config_root }}/app.config"
 arteria_bcl2fastq_logger_config: "{{ arteria_bcl2fastq_config_root }}/logger.config"
 bcl2fastq_logs_path: /var/log/bcl2fastq/
 
+arteria_bcl2fastq_bcl2fastq_install_path: /usr/local/bin/bcl2fastq
+
+
 # TODO: Temporary off, should be on if arteria_environment == `staging`
 arteria_bcl2fastq_run_tests: False
 

ansible-st2-local/roles/bcl2fastq/templates/bcl2fastq_app.config.j2

@@ -4,14 +4,16 @@
 bcl2fastq:
   versions:
     2.17.1:
-      binary: /usr/local/bin/bcl2fastq
+      binary: {{ arteria_bcl2fastq_bcl2fastq_install_path }}
       class_creation_function:  _get_bcl2fastq2x_runner
-    2.15.2:
-      binary: /path/to/bcl2fastq
-      class_creation_function:  _get_bcl2fastq2x_runner
-    1.8.4:
-      binary: /path/to/bcl2fastq
-      class_creation_function: _get_bcl2fastq1x_runner
+# If you wish to deploy multiple versions, you can specify them like
+# in the example below.
+#    2.15.2:
+#      binary: /path/to/bcl2fastq
+#      class_creation_function:  _get_bcl2fastq2x_runner
+#    1.8.4:
+#      binary: /path/to/bcl2fastq
+#      class_creation_function: _get_bcl2fastq1x_runner
 
 machine_type:
   HiSeq X: