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
• environmental sequence sets (polysample)

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 17 or a newer version. Please go here to learn more:

https://openjdk.org/install/

The program is run using the java command:

java -jar <webin-cli-jar-file> <options>

for example:

java -jar webin-cli-9.0.3.jar -help

To increase the memory available to Webin-CLI please use the -Xms java option:

java -Xms2G -jar <webin-cli-jar-file> -help

Docker

Run

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

Publishing

• Create docker image with default tags by running gradle dockerTag

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 :

gradle publish

Support

Please contact ENA helpdesk for bugs, features and other issues related to this tool.