Revision as of 12:36, 27 November 2016

Windows 10 Bash shell

Gene counting and variant call (both Samtools and GATK) works fine. For variant annotation, see the comment #2 below.

Need to install Xming. Before calling ./SeqTools from the Bash shell, run export DISPLAY=:0 first.
Automatic setup:
- Need to install unzip utility sudo apt-get install unzip.
- Java JDK from ppa:webup8team does not work. We need to install it from Oracle website. To make the installation silently, we need to change the bash script sudo tar xzvf /mnt/c/Users/brb/Downloads/jdk-8u112-linux-x64.tar.gz. Also edit ~/.bashrc file to make the java available from a global environment.
- An issue in pandoc: timer-create function not implemented. In other words, if we run variant annotation, we will get a bug report message. The main output files (1 vcf and 2 texts files) are generated but the pdf/html files cannot be created.

See Tools Manager -> Automatic setup. A developer version of the shell script is available on Github.

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	[https://linus.nci.nih.gov/seqtools/ BRB-SeqTools]		Wiki for [https://linus.nci.nih.gov/seqtools/ BRB-SeqTools]

	= [https://msdn.microsoft.com/en-us/commandline/wsl/about Windows 10 Bash shell] =		= [https://msdn.microsoft.com/en-us/commandline/wsl/about Windows 10 Bash shell] =