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Installing geofetch

Installing geofetch

Releases are posted as GitHub releases, or you can install from PyPI using pip:

pip install geofetch

Confirm it was successful by running it on the command line:

geofetch --help

If the executable in not in your $PATH, append this to your .bashrc or .profile (or .bash_profile on macOS):

export PATH=~/.local/bin:$PATH

Prerequisites for SRA data downloading

To download raw data You must have the sratoolkit from NCBI installed, with the tools in your PATH. Once it's installed, you should check to make sure you can run prefetch. Also, make sure it's configured to store SRA files where you want them. For more information, see how to change sratools download location.

Setting data download location for sratools

geofetch is using the sratoolkit to download raw data from SRA -- which means it's stuck with the default path for downloading SRA data, which is in your home directory. So before you run geofetch, make sure you have set up your download location to the correct place. In our group, we use a shared group environment variable called ${SRARAW}, which points to a shared folder (${DATA}/sra) where the whole group has access to downloaded SRA data. You can point the sratoolkit (and therefore geofetch) to use that location with this one-time configuration code:

echo "/repository/user/main/public/root = \"$DATA\"" > ${HOME}/.ncbi/user-settings.mkfg

Now sratoolkit will download data into an /sra folder in ${DATA}, which is what ${SRARAW} points to.

If you are getting an error that the .ncbi folder does not exist in your home directory, you can just make a folder .ncbi with an empty file user-settings.mkfg and follow the same command above.