创建环境

• 编辑tremolo.yml文件，内容如下：

name: TrEMOLO
channels:
 - conda-forge
 - bioconda
 - defaults
dependencies:
 - blast=2.9.0
 - bedtools=2.27.1
 - samtools
 - assemblytics
 - snakemake=5.10.0
 - minimap2
 - sniffles=1.0.12
 - svim=1.4.2
 - coreutils=8.30
 - r-base
 - r-knitr
 - r-rmarkdown
 - r-bookdown
 - r-viridis
 - r-viridisLite
 - r-rjson
 - r-ggthemes
 - r-forcats
 - r-reshape2
 - r-dplyr
 - r-kableExtra
 - r-extrafont
 - r-ggplot2
 - r-RColorBrewer
 - r-stringr
 - r-stringi
 - python=3.8.10
 - pip
 - nodejs=12.10.0
 - pip:
   - biopython
   - pandas
   - numpy
   - matplotlib
   - intervaltree

• 创建conda环境

conda env create -f tremolo.yml
或
mamba env create -f tremolo.yml

• 启动环境

conda activate TrEMOLO

• 安装RaGOO

cd /path/to/conda/env/TrEMOLO/opt/
git clone https://github.com/malonge/RaGOO.git
cd RaGOO
python setup.py install

• 安装TrEMOLO

cd /path/to/conda/env/TrEMOLO/opt/
git clone https://github.com/DrosophilaGenomeEvolution/TrEMOLO.git

修改环境

• 安装samtools

# 安装samtools 1.15.1
cd /path/to/conda/env/TrEMOLO/bin
wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
tar zxvf samtools-1.15.1.tar.bz2
cd samtools-1.15.1
./configure
make

# 安装samtools 1.9
cd /path/to/conda/env/TrEMOLO/bin
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar jxvf samtools-1.9.tar.bz2
cd samtools-1.9
./configure
make

# 删除创建环境时产生的samtools
rm /path/to/conda/env/TrEMOLO/bin/samtools

• 修改TrEMOLO

# 打开/path/to/conda/env/TrEMOLO/opt/TrEMOLO/env.sh在开头添加
SAMTOOLS_1_9=/path/to/conda/env/TrEMOLO/bin/samtools-1.9
SAMTOOLS=/path/to/conda/env/TrEMOLO/bin/samtools-1.9
SAMTOOLS_1_15_1=/path/to/conda/env/TrEMOLO/bin/samtools-1.15.1
export PATH=$SAMTOOLS:$PATH

#打开/path/to/conda/env/TrEMOLO/opt/TrEMOLO/lib/python/parse_blast_main.py，修改152行
df = pd.read_csv(name_file, "\t", header=None)
# 为
df = pd.read_csv(name_file, sep="\t", header=None)

测试TrEMOLO

conda activate TrEMOLO
cd /path/to/conda/env/TrEMOLO/opt/
snakemake --snakefile TrEMOLO/run.snk --configfile TrEMOLO/test/tmp_config.yml