Initialization

Initializing using required arguments

After you have installed spacemake as specified here, you are ready to process and analyze spatial samples.

To initialize spacemake cd into the directory in which you want to start spacemake. This directory will be your project_root.

Then simply type:

spacemake init \
   --dropseq_tools <path_to_dropseq_tools_dir>

Here the path_to_dropseq_tools_dir should point to the directory of the downloaded Dropseq-tools package, downloaded in Step 2 of the installation.

Optional arguments

The spacemake init command takes the following optional arguments:

root_dir

The root_dir for the spacemake instance. Defaults to ., the directory in which spacemake init is ran.

temp_dir

Path to the temporary directory, defaults to /tmp.

download_species

If set, spacemake will download the genome (.fa) and annotation (.gtf) files for mouse and human (from gencode, as specified here.

Hence, the complete spacemake init command looks like this:

spacemake init \
  --root_dir ROOT_DIR \             # optional
  --temp_dir TEMP_DIR \             # optional
  --download_species \              # optional
  --dropseq_tools DROPSEQ_TOOLS     # required