The bioBakery help forum

How to install biobakery_workflows database manually

Thank you very much for your excellant software pipeline biobakery_workflows! I have installed the biobakery_workflows through docker. The website (https://github.com/biobakery/biobakery/wiki/biobakery_workflows) has explained the biobakery_workflows databases installation,however, it seems unclear. For example, If I have downloaded the corresponding databases, then, how to set the below environment variables in Docker. Shotgun workflows: KNEADDATA_DB_HUMAN_GENOME, KNEADDATA_DB_RIBOSOMAL_RNA, KNEADDATA_DB_HUMAN_TRANSCRIPTOME, STRAINPHLAN_DB_REFERENCE, and STRAINPHLAN_DB_MARKERS. 16s workflows: GREEN_GENES_USEARCH_DB, GREEN_GENES_FASTA_DB, and GREEN_GENES_TAXONOMY_DB. Would you help me? Thank you very much!

Hi user,

One way to set the environment variables in docker would be to use the -e flag during the docker run.

For example, the following docker run command would set the KNEADDATA_DB_HUMAN_GENOME and KNEADDATA_DB_RIBOSOMAL_RNA environment variable to the specified path.

docker run -it \
 -e KNEADDATA_DB_HUMAN_GENOME =$PATH_OF_HUMAN_DATABASE_FILE \
 -e KNEADDATA_DB_RIBOSOMAL_RNA =$PATH_OF_RIBOSOMAL_DATABASE_FILE
biobakery/workflows bash

The other way would be export the PATH inside the docker container. Please not that these environment variables will not be persistent will need to be exported again if the docker container is refreshed.

$ docker run -it biobakery/workflows bash
$ export KNEADDATA_DB_HUMAN_GENOME=$PATH_OF_HUMAN_DATABASE_FILE
$ export KNEADDATA_DB_RIBOSOMAL_RNA =$PATH_OF_RIBOSOMAL_DATABASE_FILE
$ source ~/.bashrc

Thanks,
Sagun Maharjan

Dear Dr. Sagun Maharjan´╝î
Thank you very much for your quick reply!
Best regards

Li Zhihua