/scripts/00_get_tools_and_export_paths.txt

Version 1

# zagor

## create folder for busco, dependencies and busco DB, named here /path/to/your/BUSCOrelatedFiles/


### DB
# get busco DB
wget http://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz


### TOOLS
# install boost
# https://www.boost.org/doc/libs/1_60_0/more/getting_started/unix-variants.html
wget http://sourceforge.net/projects/boost/files/boost/1.60.0/boost_1_60_0.tar.gz

# copy hmmer from anaconda/pkgs/hmmer-3.1b2-3/

# get zlib
wget http://www.zlib.net/zlib-1.2.11.tar.gz

# get bamtools
# https://github.com/pezmaster31/bamtools/wiki/Building-and-installing
git clone git://github.com/pezmaster31/bamtools.git

# install samtools, bcftools and htslib
wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2
wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2
wget https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2

# get augustus
wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz

# get busco
git clone https://gitlab.com/ezlab/busco.git


### EXPORT PATHS
export BUSCO_CONFIG_FILE="/path/to/your/BUSCOrelatedFiles/busco/config/config.ini" \
export PATH="/path/to/your/BUSCOrelatedFiles/boost_1_60_0/:$PATH" \
export LD_LIBRARY_PATH=/path/to/your/BUSCOrelatedFiles/boost_1_60_0/stage/lib/:$LD_LIBRARY_PATH \
export PATH="/path/to/your/BUSCOrelatedFiles/tools/htslib/bin:$PATH" \
export PATH="/path/to/your/BUSCOrelatedFiles/tools/bcftools/bin:$PATH" \
export PATH="/path/to/your/BUSCOrelatedFiles/tools/samtools/bin:$PATH" \
export PATH="/path/to/your/BUSCOrelatedFiles/augustus-3.3.1/bin:$PATH" \
export PATH="/path/to/your/BUSCOrelatedFiles/augustus-3.3.1/scripts:$PATH" \
export AUGUSTUS_CONFIG_PATH="/path/to/your/BUSCOrelatedFiles/augustus-3.3.1/config" \
export PATH="/path/to/your/BUSCOrelatedFiles/hmmer-3.1b2-3/bin:$PATH"