Webin command line submission interface (Webin-CLI)
Introduction
Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). Webin submission account credentials are required to use the program.
The following types of submissions are supported:
- genome assemblies
- transcriptome assemblies
- annotated sequences
- read data submissions (Fastq, BAM, CRAM)
- taxonomy reference sets
For further information about Webin-CLI please refer to:
https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html
Executable Java JAR
The latest version of the Webin-CLI can be downloaded from:
https://github.com/enasequence/webin-cli/releases
The program requires Java 1.8 or a newer which can be downloaded from:
The program is run using the java command:
java -jar webin-cli-<version>.jar <options>
for example:
java -jar webin-cli-2.0.0.jar -help
To increase the memory available to Webin-CLI please use the -Xms java option:
java -Xms2G -jar webin-cli-2.0.0.jar -help
Docker file
Since version 1.8.12 Webin-CLI is available as a docker image:
docker pull enasequence/webin-cli
docker run --rm -v <local data directory>:/data enasequence/webin-cli -help
To increase the memory available to Webin-CLI please set the JAVA_TOOL_OPTIONS environment variable:
docker run --rm -v <local data directory>:/data -e JAVA_TOOL_OPTIONS="-Xms2G" enasequence/webin-cli -help
Testing
Testing requires the following environmental variables to be set:
- webin-cli-username or webinCliUsername
- webin-cli-password or webinCliPassword
Library Jar Publishing
To publish webin-cli as a library (slim/regular jar) :
gradlew jar publish -x bootJar
Note : '-x bootJar' is important as it excludes execution of Spring's Boot jar task which creates a fat jar instead.