OptiType(v1.3.3)
Precision HLA typing from next-generation sequencing data
(一)需要安装的依赖软件或库
1. Python 2.7
2. RazerS 3
3. Samtools
4. HDF5
5. GLPK
1. Python 2.7(跳过)
2. Razers 3 (source: seqan/apps/razers3 at master · seqan/seqan · GitHub)
RazerS 3 is a tool for mapping millions of short genomic reads onto a reference genome. It was designed with focus on mapping next-generation sequencing reads onto whole DNA genomes
安装步骤:
1) git clone GitHub - seqan/seqan: SeqAn's official repository. 2) mkdir seqan/buld; cd seqan/build 3) cmake .. -DCMAKE_BUILD_TYPE=Release 4) make razers3 5) ./bin/razers3 --help
3. Samtools 1.16.1 (source: SAMtools/BCFtools/HTSlib - Downloads)
Samtools is a suite of programs for interacting with high-throughput sequencing data.
安装步骤:
1) tar -jvxf samtools-1.16.1.tar.bz2 2) cd samtools-1.16.1 3) ./configure 4) make 5) make install(如需管理员权限,sudo make install)
4. HDF5 (source: HDF5® Source Code - The HDF Group)
High-performance data management and storage suite.
安装步骤:
1) tar -jvxf hdf5-1.12.2.tar.bz2 2) cd hdf5-1.12.2 3) ./configure 4) make 5) make install(如需管理员权限,sudo make install)
5. GLPK (source: GLPK - GNU Project - Free Software Foundation (FSF))
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.
安装步骤:
1) tar -zvxf glpk-5.0.tar.gz 2) cd glpk-5.0 3) ./configure 4) make 5) make install(如需管理员权限,sudo make install)
(二)需要安装的python模块
1. NumPy
2. Pyomo
3. PyTables
4. Pandas
5. Pysam
6. Matplotlib
7. Future
Tip:在安装pysam和tables时,出现相同错误
“Could not find a version that satisfies the requirement oldest-supported-numpy (from versions: none)”
解决办法:
安装tables时,需要安装依赖包numexpr,而numexpr用pip install numexpr命令行进行安装时,安装版本是2.8.1(从Archived: Python Extension Packages for Windows - Christoph Gohlke (uci.edu)官网查到适用于python2.7的版本,最低是2.7.1),
所以直接卸载numpy(v 1.16.6),先安装numexpr,使用命令行pip install numexpr==2.7.1,结果显示,可以正常安装,且安装依赖的numpy,版本为 1.16.6;
接下来,尝试安装官网适用于python2.7的tables版本,“pip2.7 install tables==3.5.2”——显示安装成功;
在成功安装tables后,尝试安装pysam,“pip2.7 install pysam==3.5.2”——显示安装成功;
至此,所有需要安装的python模块全部安装成功!
(三)配置config.ini文件
可以在OptiType的安装目录下,配置config.ini文件(参考config.ini.example),也可以使用-c参数来指定config.ini文件位置
(四)程序测试
利用OptiType程序自带的数据,测试OptiType的运行情况。
python OptiTypePipeline.py -i ./test/exome/NA11995_SRR766010_1_fished.fastq ./test/exome/NA11995_SRR766010_2_fished.fastq --dna -v -o ./test/exome/
结果正常。
安装完成!
参考链接:
GitHub - FRED-2/OptiType: Precision HLA typing from next-generation sequencing data