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courseInstall.sh
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courseInstall.sh
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###Get repository of the course.
#git clone https://github.com/bioinformatics-core-shared-training/cruk-bioinf-sschool.git
sudo apt-get install -y git samtools tophat sra-toolkit pkg-config bwa wget bedtools python-dev
#cd cruk-bioinf-sscchool
samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/other_exome_alignments/HG00096/exome_alignment/HG00096.mapped.illumina.mosaik.GBR.exome.20111114.bam 22 | samtools view -bS - > Day2/HG00096.chr22.bam
samtools index Day2/HG00096.chr22.bam
rm HG00096.mapped.illumina.mosaik.GBR.exome.20111114.bam.bai
samtools sort -n Day2/HG00096.chr22.bam Day2/HG00096.chr22.namesorted
bamToFastq -i Day2/HG00096.chr22.namesorted.bam -fq Day1/test.reads_1.fq -fq2 Day1/test.reads_2.fq
rm Day2/HG00096.chr22.namesorted.bam
##Download required R packages. Assumes R 3.2.0
R -f installBiocPkgs.R
##Remove some files that came from git
rm -r images javascripts stylesheets params.json index.html
##Get example breast cancer data for the first practical and put in Practicals folder
mkdir Day1/nki
wget https://www.dropbox.com/s/82p2dcwwo3qnf21/nki.zip -P Day1/nki
cd Day1/nki
unzip nki.zip
rm nki.zip
wget https://www.dropbox.com/s/b8gix98mzlzdrqq/SRR576933.fastq.gz -P Day1
cd ../../
cd Software
##Get latest version of bowtie and tophat
wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/bowtie2-2.2.5-linux-x86_64.zip
unzip bowtie2-2.2.5-linux-x86_64.zip
wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz
gunzip tophat-2.1.0.Linux_x86_64.tar.gz
tar xvf tophat-2.1.0.Linux_x86_64.tar
#### Get and compile fastx toolkit
wget https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz
gunzip libgtextutils-0.7.tar.gz
tar -xvf libgtextutils-0.7.tar
cd libgtextutils-0.7
./configure
make
sudo make install
cd ../
wget http://cancan.cshl.edu/labmembers/gordon/files/fastx_toolkit-0.0.14.tar.bz2
tar -xjf fastx_toolkit-0.0.14.tar.bz2
cd fastx_toolkit-0.0.14
./configure
make
sudo make install
wget https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py
sudo pip install cython
sudo pip install cutadapt
sudo pip install Numpy
sudo pip install MACS2
cd ../ref_data
wget http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz
gunzip chr22.fa.gz
bwa index chr22.fa
../Software/bowtie2-2.2.5/bowtie2-build chr22.fa chr22
cd ../