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Installation_guide.md

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Installation guide for Genome Skim processing pipelines

Important Note on Conda: Most of the tools would be installed through the conda distribution within an activated conda environment in the working shell.

  • Whenever you are using any of the pipelines, make sure that you change the env name in the conda_source.sh script. Refer to CONDAENV=GSkim4 in the script where GSkim4 should be changed to your environment's name corresponding to all the tool installations.
  • In the example below, we would change the conda_source.sh script to say CONDAENV=tutorial

The conda_source.sh script is meant to allow users to edit the name of their conda environment to easily switch between various configurations. A sample conda environment configuration can be seen here.

Important note on Gurobi : To be able to run Gurobi and RESPECT, you will need to create an academic license through this link. It will direct you to create an account and request a free academic license. At the end, it generates a code for you to run with grbgetkey command (ex. grbgetkey 253e22f3-...) that you can run in your terminal. This creates a license file and writes it to a default location (press Enter when it asks if you want to store it to the default location). When Gurobi is run, it looks for the license file in the defualt locations. On the expiration of the license, you will have to repeat the procedure after removing the gurobi.lic file from its default location.

Important note on Git : To be able to clone the repository, you will need to setup your public SSH key on your Github profile. If not done, you can follow the steps here under "Generating a new SSH key" and then, following the steps here under "Adding a new SSH key to your account".

Install main tools

mkdir tutorial
cd tutorial

conda create --name tutorial
conda activate tutorial

### Order matters here
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels https://conda.anaconda.org/gurobi

### Instal Skmer
conda install skmer==3.2.1
skmer -h

### The following tools should ideally be installed along with skmer. 
###If not, you can always run this command to install them separately.
conda install jellyfish seqtk mash 

###Run this command to install gurobi solver for respect
conda install gurobi 

### Install RESPECT
git clone https://github.com/shahab-sarmashghi/RESPECT.git
cd RESPECT
python setup.py install
cd ..

### BBMap has been made available as a part of the repository and you can use it directly when we clone the repository later
### You can always run the code below to download BBMap separately, if you want to
### wget -O bbmap.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz/download
### tar xvfz bbmap.tar.gz
### rm bbmap.tar.gz

### FastME has been made available as a part of the repository and you can use it directly when we clone the repository later
### You can also install FastME (to get backbone trees) separately using the following commands
### wget http://www.atgc-montpellier.fr/download/sources/fastme/fastme-2.1.5.tar.gz
### tar xvfz fastme-2.1.5.tar.gz
### chmod +x fastme-2.1.5/binaries/fastme-2.1.5-linux64
### Change "linux64" at the end if using other platforms (linux32 or windows).
### ./fastme-2.1.5/binaries/fastme-2.1.5-linux64 -h

###Cloning the repository 
git clone [email protected]:smirarab/skimming_scripts.git

###Running the pipeline on sample data
###Remember to edit the conda_source.sh file (~/tutorial/skimming_scripts/conda_source.sh) with your env name; tutorial here
###Keeping all the pipelines in the same directory would be recommended
cd skimming_scripts/test
var=`pwd`
bash ../skims_processing_pipeline.sh -x $var/skims