Revision as of 16:06, 28 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.
- 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.

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

@@ Line 9: / Line 9: @@
 #* 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 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.
+#* 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 [https://javaguru.fi/unattended-java-install-ubuntu-14-04.html here] for apt-get approach and [https://www.digitalocean.com/community/tutorials/how-to-manually-install-oracle-java-on-a-debian-or-ubuntu-vps here] for tarball approach.
 #* An issue in pandoc: [https://groups.google.com/forum/#!msg/pandoc-discuss/BI51p5YKpa0/mO5xowuZAwAJ 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.