- ngs_toolkit comes with two programs that provide a command line interface (CLI):
projectmanager
handles the creation and execution of a looper project, providing sensible configuration templates and git-enabled tracking of changes.trackmanager
handles the creation of a UCSC trackhub or IGV link for ATAC/ChIP-seq data based on bigWig files created bylooper
pipelines.
Here you can see the command-line usage instructions for the main looper command and for each subcommand:
usage: projectmanager [-h] {create,recipe} ...
projectmanager - A project manager.
positional arguments:
{create,recipe}
create Create project.
recipe Run ngs_toolkit recipe for a given project.
optional arguments:
-h, --help show this help message and exit
https://github.com/afrendeiro/toolkit
usage: projectmanager create [-h] [-r ROOT_DIR] [-d] [--overwrite]
project_name
Create project.
positional arguments:
project_name Project name.
optional arguments:
-h, --help show this help message and exit
-r ROOT_DIR, --root-dir ROOT_DIR
Root directory to create projects.
-d, --dry-run Don't actually do anything.
--overwrite Don't overwrite any existing directory or file.
usage: projectmanager recipe [-h] recipe_name project_config
Run recipe.
positional arguments:
recipe_name Recipe name.
project_config Project config.
optional arguments:
-h, --help show this help message and exit
usage: trackmanager [-h] [-a [ATTRIBUTES]] [-c COLOR_ATTRIBUTE] [-r] [-l]
project_config_file
positional arguments:
project_config_file
optional arguments:
-h, --help show this help message and exit
-a [ATTRIBUTES], --attrs [ATTRIBUTES]
Sample attributes (annotation sheet columns) to use to
order tracks. Add attributes comma-separated with no
whitespace.
-c COLOR_ATTRIBUTE, --color-attr COLOR_ATTRIBUTE
Sample attribute to use to color tracks with. Default
is first attribute passed.
-r, --overlay-replicates
Whether replicate samples should be overlaied in same
track. Default=False.
-l, --link Whether bigWig files should be soft-linked to the
track database directory. Default=False.
Note
Copying vs linking bigWig files files in trackmanager
The intention of trackmanager is to create a hierarchy of files in a HTTP server which can be used by genome browsers. This requires files (and their parent directories) to be readable and executable. When soft-linking files, they will retain the permission attributes of the original files and this may not be appropriate to serve through a server. Be aware that copying or linking these files does not always works (manual movement of files might be required).
Note
Changing permissions of files and directories in bigwig directory
Trackmanager will try to change the permissions of the bigwig files and their parent directories to allow reading and execution by everyone. Be aware that this does not always works (manual permission changes might be required).