Seqtools
Jump to navigation
Jump to search
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.
Software List
See Tools Manager -> Automatic setup. A developer version of the shell script is available on Github.
Program | Major language | Version |
---|---|---|
bowtie2 | C++ | 2.2.6 |
tophat | C++ | 2.1.0 |
bwa | C | 0.7.12 |
star | C++ | 2.5.1b |
picard | Java | 1.141 |
samtools | C | 1.3 |
gatk | Java | 3.6 |
bcftools | C | 1.3 |
htslib | C | 1.3 |
annovar | Perl | 2016Feb01 |
sratoolkit | Shell | 2.7.0 |
fastqc | Java | 0.11.5 |
fastx | C | 0.0.13 |
snpeff | Java | 4_2 |
htseq | Python | 0.6.1p1 |
R | R | 3.3.x |
pandoc | Haskell | 1.16.0.2 |
latex, lftp, avfs | Ubuntu repository |