As an example, we provide the following youtube-dl command line call to download a playlist:5.
In all cases, each command line call to blastn involved one query.
The algorithm is invoked via a single command line call, which outputs a list of uncolored taxa for every nonconvex taxonomic rank as well as displaying them on a taxonomically labeled tree by highlighting them in red.
Such methods not implemented in Python can be plugged in using command-line calls.
The entire suite of applications also includes Differential, a code review tool that allows developers to easily submit reviews to one another via a command line tool called Arc when they check in code using Git or Subversion, Phriction a wiki tool which integrates more and more with Maniphest, and a slew of other products, all designed and described in Phabricator's unique voice.
To facilitate the application of our network-based approach to additional cancer types, we have made our software freely available as part of a command line tool, called NetBox.
The command line for calling WEKA is shown as follows.
The main Perl program, seq_router.pl, processes command line parameters and calls sequence analysis, domain boundary detection, and domain-processing modules for individual protein sequences.
Altogether, we included the following methods for comparison (for corresponding command lines for calling the five algorithms, see Additional file 1): 1. NaiveSubtract — SNVs were called separately from virtual tumor and normal samples using GATK UnifiedGenotyper [ 22].
We used following command lines to call MEIs on simulation dataset with RetroSeq: The source code and documentation are available at https://github.com/jiantao/Tangram. Tangram is also available as part of our pipeline and tool launcher system, GKNO, which is available at https://github.com/gkno.
