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Software for tutorial on gene prediction #2

Open LizzyGe opened 8 years ago

LizzyGe commented 8 years ago

Dear Casey, this is the list of software the students will need to have access to during the practical lesson on gene prediction, that I will give on 2 June. Let me know if there is anything unclear about the links or tools. Thank you for the installation. Kind regards, Lizzy

  1. gene Prediction tool AUGUSTUS The binaries augustus, etraining and bam2hints (auxprogs) need to be compiled and put in the path as well as the augustus/scripts directory, furthermore the AUGUSTUS config directory needs to be set as environement variable: export AUGUSTUS_CONFIG_PATH=/path/to/your/installation/config/
  2. The RNA-Seq spliced aligner STAR
  3. bamtools
  4. wigToBigWig
  5. BRAKER1
caseywdunn commented 8 years ago

I am installing these with the following commands:

bib install bamtools
mkdir src
mkdir bin
echo "export PATH=~/bin:\$PATH" >>~/.profile
source ~/.profile
cd src
# bamtools, needed for augustus
# http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/bamtools.htm
git clone https://github.com/pezmaster31/bamtools
cd bamtools
mkdir build
cd build
cmake ..
make
sudo make install
echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/bamtools" >>~/.profile
source ~/.profile

# Augustus
sudo apt-get install libboost-iostreams-dev
cd ~/src
wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz
gunzip augustus.current.tar.gz
tar -xvf augustus.current.tar
cd augustus-3.2.2/
make # this errors with - bam2hints.cc:16:27: fatal error: api/BamReader.h: No such file or directory

# STAR
# Tried making first, then went htis route. But looks like build did install at /home/ubuntu/bin/STAR
cd ~/src
wget https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz
tar -xzf STAR_2.4.2a.tar.gz
cp STAR-STAR_2.4.2a/bin/Linux_x86_64/STAR ~/bin
cp STAR-STAR_2.4.2a/bin/Linux_x86_64/STARlong ~/bin

# wigToBigWig
# wasn't sure which target to isntall

# BREAKER1
# Requires AUGUSTUS
LizzyGe commented 8 years ago

Here's what I did to get everything work: installation_make.txt

LizzyGe commented 8 years ago 
# installed current release of STAR
cd ~/src
wget https://github.com/alexdobin/STAR/archive/2.5.2a.tar.gz
tar xvf 2.5.2a.tar.gz
cp STAR-2.5.2a/bin/Linux_x86_64/STAR  STAR-2.5.2a/bin/Linux_x86_64/STARlong ~/bin/

# changed LD_LIBRARY_PATH to local installation in ~/.profile
export LD_LIBRARY_PATH=:$HOME/src/bamtools/lib/
LizzyGe commented 8 years ago 
# install samtools

git clone https://github.com/samtools/htslib.git
make
make install
git clone git://github.com/samtools/samtools.git
make
make install