setup instr

SETUPINSTR.md

+# Basic
+
+The following guide is written for a Linux based system. Enhort runs on Java 8 and needs a SQlite database to store information about available tracks.
+It is recommended to download and use the pre-build database.
+
+For full usage it is recommended to have server with about 32 GB Mem for the current database. However, Enhort is capable of beeing run on a small PC or server with less annotation tracks.
+
+Enhort is build to run on two different servers, a computation back-end server and a visibile front-end server. However, it is possible to run both on the same server. Use 127.0.0.1 as ip then.
+
+# Database 
+
+### Use pre-build database
+Download the SQlite database and the corresponding .bed tracks from .... Save the database and the data files in a known directory.
+
+### Build own database
+TODO 
+
+# Server setup
+Download the enhort.jar from ....
+
+
+### Run the server
+The server is run with the following command:
+
+    java -jar -Xmx32g -XX:StringTableSize=1000003 /path/to/server/jar/enhort.jar /path/to/data/directory/  /path/to/database.db
+
+
+- The -Xmx32g flag raises the available memory to 32 GB, please specify your available memory here. 
+- The StringTableSize improves start up speed for loading the data
+- Currently the port is fixed to 42412
+
+
+# Frontend setup
+Download the frontend archive containing the .jar and the contig sizes for hg19 and hg38.
+The frontend is run with the following command:
+
+    java -Xmx2g -Dmultipart.maxFileSize=20MB -Dmultipart.maxRequestSize=20MB -Dspring.profiles.active=production -jar frontend.jar 127.0.0.1 /path/to/contig/size/files /path/to/logfile/enhort.log
+
+- You can specify the maximum allowed upload file size
+- You need to specify the address of the backend server. If both are run on the same server use 127.0.0.1
+- The path to the contig sizes .bed file is needed
+- A log file is written at the given location
+
+
+
+# Misc
+
+### Encryption
+TODO 

frontend/src/main/java/de/thm/spring/backend/Settings.java

+package de.thm.spring.backend;
+
+public class Settings {
+}