ngless’ results do not change because of configuration or command line options. The ngless script always has complete information on what is computed. What configuration options change are details of how the results are computed such as where to store intermediate files and how many CPU cores to use.
Ngless gets its configuration options from the following sources:
- A global configuration file
- A user configuration file (typically
- A configuration file present in the current directory`
- A configuration file specified on the command line
- Command line options
In case an option is specified more than once, the order above determines priority: later options take precedence.
Configuration file format¶
NGLess configuration files are text files using assignment syntax. Here is a simple example, setting the temporary directory and enabling auto-detection of the number of threads:
temporary-directory = "/local/ngless-temp/" jobs = "auto"
jobs: number of CPUs to use. You can use the keyword
auto to attempt
auto-detection (see below).
strict-threads: by default, NGLess will, in certain conditions, use more
CPUs than specified by the
jobs argument (in bursts of activity). This
happens, for example, when it calls an external short-read-mapper (such as bwa). By default, it will pass the
threads argument through to
bwa. However, it will still be processing
bwa’s output using its own threads. This will results in small bursts of
activity where the CPU usage is above
jobs. If you specify
--strict-threads, however, then this behavior is curtailed and it will
never use more threads than specified (in particular, it will call
using one thread fewer than specified, while restricting itself to a single
thread, thus even peak usage is at most the number of specified threads).
temporary-directory: where to keep temporary files. By default, this is the
system defined temporary directory (either
/tmp or the value of the
$TEMPDIR environment variable on Unix).
color: whether to use color output. Defaults to
auto (i.e., print color
if the output is a terminal),
no (never use color),
force (use color even
if writing to a file or pipe),
yes (synonym of
print-header: whether to print ngless banner (version info…).
user-directory: user writable directory to cache downloads (default is
system dependent, on Linux, typically
user-data-directory: user writable directory to cache data (default is a
data directory inside the
user-directory [see above]).
index-path: user writable directory to store indices and similar data.
global-data-directory: global data directory.
keep-temporary-files: whether to keep temporary files after the end of the programme.
trace (only command line): print a lot of internal information.
Auto-detection of the number of CPUs¶
If the option
auto is passed as the number of jobs (either on the command
line or in the configuration file), ngless will inspect the environment looking
for a small set of clues as to how many CPUs to use. In particular, it will
make use of these variables:
If none are found (or they do not contain a single number), an error is produced.