Seqtools: Difference between revisions
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= [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] = | ||
Gene counting and variant call works fine. | 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: [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. | |||
Revision as of 12:13, 22 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.