Installation of tools to work with skimming data

Installations

The following steps show how to install the tools.

• If you are unable to follow some of the steps, a lot of the outputs (all the smaller files) are provided here as a zip file you can download: Skmer+APPLES+tutorial-smallfiles.zip

Main tools:

• Skmer
• APPLES
• MISA
• RESPECT
• CONSULT

Other tools we will use:

• ART
• Kraken-II
• FastME
• FastTree-II
• guppy
• Newick utilities

Install on a new machine or locally

• Instructions shown below work on Linux. Some changes are needed for MAC and Windows. See comments.

conda create --name skmer
conda activate skmer

conda config --add channels bioconda

### Instal Skmer
conda install skmer
skmer -h

### Instal APPLES
python -m pip install -U apples
run_apples.py -h
python -m pip  list |grep apples
### If you have versions older than 1.3.0, you may need to updating using:
python -m pip install --upgrade apples

### Install MISA
python -m pip install misa
run_misa.py -h


### Install FastME (to get backbone trees)
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-inux ## Change "inux" at the end if using other platforms (osx or windows).
./fastme-2.1.5/binaries/fastme-2.1.5-osx -h

### install fasttree
wget http://www.microbesonline.org/fasttree/FastTree.c
gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
### Note: for linux, you can find binary files on the FastTree website
./FastTree -h

### Guppy for working with .jplace files
wget https://github.com/smirarab/sepp/raw/master/tools/bundled/Linux/guppy-64
mv guppy-64 guppy
# wget https://github.com/smirarab/sepp/raw/master/tools/bundled/Darwin/guppy

chmod +x guppy
./guppy --version

### Other scripts:
wget https://raw.githubusercontent.com/balabanmetin/LSEdiag/master/tsv_to_phymat.sh
wget https://raw.githubusercontent.com/balabanmetin/misa/master/scripts/convert_to_tsv.sh
chmod +x tsv_to_phymat.sh
chmod +x convert_to_tsv.sh

### (Optional) If you want to simulate skimming, Install ART
# The link below is for MAC. For other platforms, see https://www.niehs.nih.gov/research/resources/software/biostatistics/art/
    # For MAC, it's https://www.niehs.nih.gov/research/resources/assets/docs/artbinmountrainier2016.06.05macos64.tgz
wget https://www.niehs.nih.gov/research/resources/assets/docs/artbinmountrainier2016.06.05linux64.tgz 
tar xvfz artbinmountrainier2016.06.05macos64.tgz
art_bin_MountRainier/art_illumina -h

### newick utilities
conda install -c bioconda newick_utils
conda install -c bioconda/label/cf201901 newick_utils

RESPECT

module load Jellyfish/2.3.0-GCC-9.3.0
# Note, you may need to swap GCC. Go down the rabbit hole

module load seqtk/1.3-GCC-9.3.0

python3.9 -m pip install gurobipy
# after you install gurobipy package using pip as described above, you need to set up the license; they have free academic license; see https://www.gurobi.com/documentation/9.1/quickstart_mac/creating_a_new_academic_li.html#subsection:createacademiclicense

git clone https://github.com/shahab-sarmashghi/RESPECT.git
cd RESPECT
python3.9 setup.py install
cd ..

CONSULT

Instruction for CONSULT

Instruction for CONSULT (you can go straight to query):

Installation

To install and compile search command on your machine:

git clone https://github.com/noraracht/CONSULT.git
cd CONSULT/
g++ main_search.cpp -std=c++11 -fopenmp -O3 -o consult_search