GSvar docu: updated settings related to client-server mode

bin/GSvar.ini.example

@@ -65,8 +65,9 @@ gsvar_file_outdated_before = 2021-12-01
 interpretability_regions = 
 text_editor = 
 
-#Path to the file that includes root and intermediate certificates, needed to access BAM files over HTTPS
-curl_ca_bundle = "ca-bundle.crt"
-
-#Check for the user notifications comming from the server (e.g. information about updates)
+#GSvar server
+server_host = ""
+server_port = 
+curl_ca_bundle = ""
 display_user_notifications = true
+use_proxy_for_gsvar_server = false

bin/settings.ini.example

@@ -54,9 +54,5 @@ nova_seq_x_sw_version = "4.1.23"
 nova_seq_x_app_version = "1.2.1"
 nova_seq_x_keep_fastq = 1
 
-# For accessing an external GSvar server through a proxy,
-# while using inside the internal network should be set to False
-use_proxy_for_gsvar_server = false
-
 #location, used to enable site-specific adaptations
 location = ""

doc/GSvar/configuration.md

@@ -21,7 +21,6 @@ The settings are:
 - *genlab\_...*: Database credentials for the GenLab (if available)
 - *projects\_folder\_...*: Prject data folders for different project types (diagnostic, research, test, external)
 - *data\_folder*: megSAP data folder used to find target region BED files of processing systems
-- *use_proxy_for_gsvar_server*: for using an external GSvar server should be set to True (if your network is behind a HTTP proxy server)
 
 ### GSvar.ini
 
@@ -48,6 +47,11 @@ The most important settings are:
 	- region name
 	- path to BED file
 - *text\_editor*: Path of the preferred text editor. It is e.g. used to open log files.
+- *server\_host*: The host the GSvar server is running on.
+- *server\_port*: The port the GSvar server is running on.
+- *display_user_notifications*: Flag to indicate if user notifications from the server should be shown (default is  true).
+- *curl_ca_bundle*: SSL certificate needed to access BAM/CRAM files on the server (handed to libcurl).
+- *use_proxy_for_gsvar_server*: for using an external GSvar server should be set to True (if your network is behind a HTTP proxy server)-.
 
 ## Filters