Overview¶
pycard¶
| docs | |
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| tests |    |
This script facilitates calling /path/to/picard.jar. Its purpose is to allow you to call picard without providing or even knowing the full path to the executable far file.
- Free software: MIT license
Usage¶
To use pycard in a from the command line:
$ pycard --help
Usage: pycard [OPTIONS] COMMAND [ARGS]...
This script facilitates calling `/path/to/picard.jar`.
Its purpose is to allow you to call picard without providing or even
knowing the full path to the executable far file.
Options:
--use-path PATH Provide a path to override the default picard.jar location.
--version Show the version and exit.
--help Show this message and exit.
Commands:
do runs picard
help shows the picard.jar help text
$ pycard do --help
Usage: pycard do [OPTIONS] [PICARD_ARG]...
This command actually calls picard.
PICARD_ARG These will be passed directly to picard.
The help text for picard can be accessed by providing zero PICARD_ARGs.
Example usages:
pycard do PicardCommandName OPTION1=value1 OPTION2=value2...
pycard do --jvm-args '-Xmx6g' PicardCommandName OPTION1=value1 OPTION2=value2...
pycard do PicardCommandName OPTION1=value1 OPTION2=value2... --jvm-args '-Xmx6g'
Options:
--jvm-args TEXT a quoted string that contains the args you wish to pass to
the java virtual machine. [default: '-Xmx2g']
--help Show this message and exit.
Installation¶
Danger
There is a PyCard on PyPI, but that is NOT this package!
Do NOT simply pip install pycard or you will end up with that address card program!
git clone https://github.com/xguse/pycard.git
cd pycard
pip install .
Or via conda:
conda install pycard -c http://xguse.github.io/conda-package-repo/pkgs/channel/