Configuration¶
There are various aspect of pype that can be configured. Notably the installation paths of the modules are the most common variables that needs to be set.
By default the pype modules (snippets, pipelines, profiles and queues) are installed in the python library installation, within the package site-packages folder.
Retrieving the modules in the installation folder can made unnecessarily cumbersome to add/edit/change modules.
Configuring different paths for the modules, it also makes possible to easily switch from a set of modules to another (eg from a “stable” to a “development” set of modules).
The set of configuration variables are listed in the section “Available variables”
Local configuration file¶
When a configuration file in ~/.bio_pype/config exists, the program will read the configuration to set the variables.
The configuration file looks like this:
PYPE_TMP=/tmp
PYPE_LOGDIR=/tmp/logs
Environment variable¶
Variables can also be set as environment variables. Setting a variable in the environment will override the corresponding variable if also set in the configuration file.
Available variables¶
| Variable | Description |
|---|---|
| PYPE_MODULES | Sets the path of pipelines, profiles, queues and snippets at a prefix with the specified folder. It also overrides the path variable for each separate module. |
| PYPE_SNIPPETS | Sets the path for the snippets module to the specified folder |
| PYPE_PROFILES | Seta the path for the profiles module to the specified folder |
| PYPE_PIPELINES | Sets the path for the pipelines module to the specified folder |
| PYPE_QUEUES | Sets the path for the queues module to the specified folder |
| PYPE_REPOS | Sets the path for the repos.yaml file to read |
| PYPE_NCPU | It can be used to set the number of maximum CPUs to use when launching jobs in parallel without using an external scheduler. |
| PYPE_MEM | It can be used to set the maximum amount of memory to use, when launching jobs in parallel without using an external scheduler |
| PYPE_TMP | Sets a temporary folder that can be used in snippets using the ‘%(pype_tmp)s’ tag (or by loading __config__.PYPE_CONFIG in python snippets) |
| PYPE_LOGDIR | Sets the path for the log files. By default is set to`~/.bio_pype/logs` |
| PYPE_DOCKER | Sets the binary to launch docker or other container-based solution. The default value is docker. I also accepts full path of the binary. It support also udocker and singularity |
| PYPE_SINGULARITY_CACHE | Sets the path for the singularity sif images. There is no default path for this variable |