Project Description¶

Admin related logistics regarding uploading and annotating data to Synapse for members of the VEOIBD consortium.

Before we begin¶

There are a few things that we take for granted at this point.

You are a registered Synapse user.
You have either Conda or Miniconda installed.
You have the ability to execute Makefiles.
- Linux/Unix/OS X should work fine out of the box.
- Windows will need Cygwin installed or take advantage of the ability to run bash in Windows 10.

Registering with Synapse ¶

Create an account at Synapse
You will need to register and become a certified user.

Installing¶

Download this project repository¶

Using git...

git clone https://github.com/ScottSnapperLab/veoibd-synapse-data-manager.git

Using your web browser...

Click here to see a list of releases.
Download and unzip.
Navigate into the project folder.

“Install” the package¶

At your terminal, in the directory we created above:

make install

Now activate the conda environment that we just created with this command:

source activate veoibd_synapse

And let’s see the program’s main help text:

$ veoibd_synapse --help
Usage: veoibd_synapse [OPTIONS] COMMAND [ARGS]...

  Command interface to the veoibd-synapse-manager.

  For command specific help text, call the specific command followed by the
  --help option.

Options:
  -c, --config DIRECTORY  Path to optional config directory. If `None`,
                          configs/ is searched for *.yaml files.
  --home                  Print the home directory of the install and exit.
  --help                  Show this message and exit.

Commands:
  configs  Manage configuration values and files.
  push     Consume a push-config file, execute described...

Configuring¶

To generate fresh example configs in the config directory, use the veoibd_synapse configs command.

Usage: veoibd_synapse configs [OPTIONS]

  Manage configuration values and files.

Options:
  -l, --list                      Print the configuration values that will be
                                  used and exit.
  -g, --generate-configs          Copy one or more of the 'factory default'
                                  config files to the top-level config
                                  directory. Back ups will be made of any
                                  existing config files.  [default: False]
  -k, --kind [all|site|users|projects|push|pull]
                                  Which type of config should we replace?
                                  [default: all]
  --help                          Show this message and exit.

See Usage for more detailed information.

To generate a full set of fresh configs, run this:

veoibd_synapse configs --generate-configs

Uploading a batch of files¶

You need to have a project created on Synapse for the files to be sent to.
You will need to have created the appropriate configuration files:
- See the config section
See Usage for more detailed information.

Lets take a look at the help text for the push command:

$ veoibd_synapse push  --help

Usage: veoibd_synapse push [OPTIONS]

  Consume a push-config file, execute described transactions, save record of
  transactions.

Options:
  -u, --user TEXT     Provide the ID for a user listed in the 'users' config
                      file.
  --push-config PATH  Path to the file where this specific 'push' is
                      configured.
  --help              Show this message and exit.

And a quick example command would be:

$ veoibd_synapse push -u GUSDUNN --push-config configs/GUSDUNN/new_WES_files.yaml