Commit 1285d412 authored by Michael Menzel's avatar Michael Menzel

instructions updated

parent 6712fd68
......@@ -24,24 +24,5 @@ Enhort is publicly available online at www.enhort.mni.thm.de and published under
# Build
Enhort is build using Maven. Some tests do not work well using mvn and need some files to be set up to work,
the build is possible by skipping the test with -DskipTests=true
A seperate SETUPINSTR.md file is available containing instructions to run Enhort on your own infrastructure.
Enhort works using a backend server and a frontend webserver. Both need to be build and deployed.
Additionally Enhort needs a sqlite database for all annotations and a directory containing the .bed files.
The current database is uploaded as example.db
A keyfile for encrypted communication needs to be created and the path changed in the BackendConnector
class of the Frontend
The connection ip to connect the Frontend to backend needs to be changed in the BackendConnector as well
as the used port.
The backend needs the used genomes as .fa files. The directory needs to be given upon start of the backend
as parameter. Example call:
```/usr/bin/java -jar -Xmx60g -XX:StringTableSize=1000003
enhort.jar
data/dir
example.db
```
......@@ -18,6 +18,8 @@ TODO
# Server setup
Download the enhort.jar from ....
Create a empty directory /logs in user home directory for logfiles
### Run the server
The server is run with the following command:
......@@ -32,14 +34,16 @@ The server is run with the following command:
# Frontend setup
Download the frontend archive containing the .jar and the contig sizes for hg19 and hg38.
Create a empty directory /logs in user home directory for logfiles
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
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/statistics/file
- 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
- A usage statistics file is written at the given location of the statistics file
......@@ -47,3 +51,8 @@ The frontend is run with the following command:
### Encryption
TODO
### Known issues
- The sample button does not work on custom systems because the .bed-file used for the sample run is not available
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