lojae.blogg.se - Bam file format example

#Bam file format example plus

In order for the tool to run properly, all parts of the base command that are separated by a space need to be entered in separate fields within the Base command section in Tool Editor.

Together, the command and subcommand form the base command. To keep the example simple, we will use the default values for most parameters and options, and aim to build a command line that looks like: samtools sort takes an input BAM-format file containing short DNA sequence reads and sorts it. In this tutorial, we’ll wrap samtools sort, one of the tools in the samtools suite. Step 1: Identify the required options for the command line

connect a Platform account and add at least one Platform project to your workspace.

Prerequisitesīefore starting this tutorial, you need to: If you are not familiar with tool wrapping, then we recommend you read that section first. This tutorial uses the concepts explained in the introduction to tool wrapping.

upload our tool to the Platform and run it as a task on the Platform.

use Rabix Executor to run and test our tool locally.

use the Rabix Composer tool editor to describe the tool and the options we are exposing.

create the Docker image containing the tool and the environment it needs to run.

identify the options for the command line tool and determine which ones we want to expose to the users in the wrapped tool.

#Bam file format example plus

20 minutes plus Platform execution time (approximately 5 minutes with smaller files and 75 minutes with larger files).