Enable sample retrieval from SRA

Check out the tool I created: https://git.scicore.unibas.ch/zavolan_group/tools/sra-download

The tool is a python wrapper that uses the command fasterq-dump from sra-tools=2.10.1.

Forgot to add link to SRA tools: https://github.com/ncbi/sra-tools

changed milestone to %upstream

Incorporate in zarp wrapper

Download public data from SRA

Installation

Download and install aspera-connect

wget -c https://download.asperasoft.com/download/sw/connect/3.9.9/ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz
tar xzvf ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz
bash ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.sh

Download and install pysradb (in a conda virtual environment)

conda create -n pysradb_python -c bioconda -c conda-forge python=3
conda activate pysradb_python
pip install git+https://github.com/saketkc/pysradb.git

Download datasets

First create the output directories

mkdir -p pysradb_info pysradb_downloads

Download the samples of a project. For example for the project SRP195779 the following command will download the samples in the directory pysradb_downloads/SRP195779

pysradb download -p SRP195779 --use_ascp

The metadata can be stored in the file pysradb_info/SRP195779.tsv with the following command

pysradb metadata SRP195779 --detailed --saveto pysradb_info/SRP195779.tsv

added To Do label

mentioned in issue #135 (closed)

added upstream label

removed To Do label

added To Do label

closed