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#* 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 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. | #* 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. | ||
= Software List = | |||
See '''Tools Manager''' -> '''Automatic setup'''. A developer version of the shell script is available on [https://github.com/arraytools/bdge/blob/master/install_rnaseq.sh Github]. | |||
{| class="wikitable" | |||
! Program | |||
! Major language | |||
! Version | |||
|- | |||
| [https://github.com/BenLangmead/bowtie2 bowtie2] | |||
| C++ | |||
| 2.2.6 | |||
|- | |||
| [https://github.com/infphilo/tophat tophat] | |||
| C++ | |||
| 2.1.0 | |||
|- | |||
| [https://github.com/lh3/bwa bwa] | |||
| C | |||
| 0.7.12 | |||
|- | |||
| [https://github.com/alexdobin/STAR star] | |||
| C++ | |||
| 2.5.1b | |||
|- | |||
| [https://github.com/broadinstitute/picard picard] | |||
| Java | |||
| 1.141 | |||
|- | |||
| [https://github.com/samtools/samtools samtools] | |||
| C | |||
| 1.3 | |||
|- | |||
| [https://github.com/broadgsa/gatk gatk] | |||
| Java | |||
| 3.6 | |||
|- | |||
| [https://github.com/samtools/bcftools bcftools] | |||
| C | |||
| 1.3 | |||
|- | |||
| [https://github.com/samtools/htslib htslib] | |||
| C | |||
| 1.3 | |||
|- | |||
| [http://annovar.openbioinformatics.org/en/latest/ annovar] | |||
| Perl | |||
| 2016Feb01 | |||
|- | |||
| [https://github.com/ncbi/sra-tools sratoolkit] | |||
| Shell | |||
| 2.7.0 | |||
|- | |||
| [http://www.bioinformatics.babraham.ac.uk/projects/download.html fastqc] | |||
| Java | |||
| 0.11.5 | |||
|- | |||
| [http://hannonlab.cshl.edu/fastx_toolkit/download.html fastx] | |||
| C | |||
| 0.0.13 | |||
|- | |||
| [https://github.com/pcingola/SnpEff snpeff] | |||
| Java | |||
| 4_2 | |||
|- | |||
| [https://github.com/pcingola/SnpEff htseq] | |||
| Python | |||
| 0.6.1p1 | |||
|- | |||
| [https://cran.r-project.org/ R] | |||
| R | |||
| 3.3.x | |||
|- | |||
| [https://github.com/jgm/pandoc pandoc] | |||
| Haskell | |||
| 1.16.0.2 | |||
|- | |||
| latex, lftp, avfs | |||
| | |||
| Ubuntu repository | |||
|} | |||
Revision as of 12:35, 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.
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 |