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.
- Install fontconfig library sudo apt-get install libfontconfig1-dev.
- New gnome-terminal windows (use apt-get install) cannot be opened from Bash shell. This affect Automatic setup tools in Tools manager and profile manager.
- Java JDK from ppa:webup8team does not work. We need to download/install it <jdk-8u112-linux-x64.tar.gz> from Oracle website. To make the installation silently, we need to add two lines to the installation script. See here for apt-get approach and here for tarball approach.
- 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.

Software List

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