Guides for ENAdumper workflows:
Installation:
It is recommended to use ENAdumper with a Conda environment
git clone https://github.com/Serka-M/ENAdumper
conda env create -f ENAdumper/src/conda.yaml -p ./ENAdumper/ENAdumper_env
cp ENAdumper/src/* ENAdumper/ENAdumper_env/bin/.
chmod +x ENAdumper/ENAdumper_env/bin/ENAdumper
Quick-start:
source activate ENAdumper/ENAdumper_env
ENAdumper --help
Full usage:
COMPRESSION INPUTS:
-fq --fastq_dir Path to directory with FastQ files
-np --fast5_dir Path to directory with Fast5 files
-n --sample Sample name
-p --processes Number of processes and fast5 batch count
UPLOAD INPUTS:
-user --webin_user Webin username
-pass --webin_pass Webin password
ENA METADATA INPUTS:
-k --key Key file with sample names and ENA sample IDs
-s --study ENA study ID
-ins --instrument_model Instrument model category
-lib_n --library_name Prefix to be used with sample name for Library name category
-lib_src --library_source Library source category
-lib_sel --library_selection Library selection category
-lib_strat --library_strategy Library strategy category
-lib_lay --library_layout Library layout category
EXTRA INPUTS:
-h --help Print help information
-v --version Print version number
Compatibility:
ENAdumper has been developed and tested on x86_64 GNU/Linux, Ubuntu 20.04