2019. 11. 6. 15:51 나의일 관련/Linux
medaka 와 기타 패키지 설치 기록
https://github.com/nanoporetech/medaka
medaka-0.10.0 버전은 아래 패키지들이 필요하다.
[의존 패키지 목록]
biopython cffi h5py==2.7.1 intervaltree tensorflow==1.14.0 numpy==1.16.1 mappy parasail pysam==0.15.2 whatshap==0.18 |
tensorflow 로 설치 하는 경우와 tensorflow_gpu 로 설치하는 경우에 따라 다르게 동작한다.
쉽게 conda 를 이용하여 CPU 버전과 GPU 버전을 설치 했다.
[CPU 버전 설치 방법]
# conda create -n medaka_cpu # source activate medaka_cpu # conda install -c bioconda medaka # conda install -c bioconda racon canu wtdbg |
[GPU 버전 설치 방법]
# conda create -n medaka_gpu # source activate medaka_gpu # conda install -c anaconda -c bioconda -c bioconda-legacy biopython mappy \ parasail-python intervaltree cffi h5py==2.7.1 tensorflow-gpu==1.14.0 \ numpy==1.16.1 pysam==0.15.2 whatshap==0.18 cudatoolkit=9.2 # conda install -c bioconda medaka racon canu wtdbg |
[테스트 방법]
- 예제 : https://s3-eu-west-1.amazonaws.com/ont-research/medaka_walkthrough_no_reads.tar.gz
# tar -xzf medaka_walkthrough_no_reads.tar.gz # cd data # medaka_consensus -d draft_assm.fa -i basecalls.fa -t 8 -b 100 |
* RTX series GPU 사용의 경우 " export TF_FORCE_GPU_ALLOW_GROWTH=true" 설정 필요하다.
[nvidia-smi 명령으로 GPU 사용 상태를 조회]
Thu Oct 31 11:10:12 2019 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 418.88 Driver Version: 418.88 CUDA Version: 10.1 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===============================+=====================| | 0 GeForce GTX 108... Off | 00000000:04:00.0 Off | N/A | | 23% 34C P2 73W / 250W | 10897MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 1 GeForce GTX 108... Off | 00000000:06:00.0 Off | N/A | | 23% 34C P2 56W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 2 GeForce GTX 108... Off | 00000000:07:00.0 Off | N/A | | 23% 30C P2 56W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 3 GeForce GTX 108... Off | 00000000:08:00.0 Off | N/A | | 23% 34C P2 56W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 4 GeForce GTX 108... Off | 00000000:0C:00.0 Off | N/A | | 23% 31C P2 55W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 5 GeForce GTX 108... Off | 00000000:0D:00.0 Off | N/A | | 23% 27C P2 55W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 6 GeForce GTX 108... Off | 00000000:0E:00.0 Off | N/A | | 23% 28C P2 55W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 7 GeForce GTX 108... Off | 00000000:0F:00.0 Off | N/A | | 23% 31C P2 56W / 250W | 147MiB / 11178MiB | 0% Default | +-------------------------------+----------------------+----------------------+ +-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |===============================+=====================| | 0 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 10887MiB | | 1 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | | 2 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | | 3 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | | 4 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | | 5 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | | 6 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | | 7 15250 C ...2/miniconda3/envs/medaka_gpu/bin/python 137MiB | +-----------------------------------------------------------------------------+ |
GPU 버전 패키지 추가 설치
$ conda install "cython>=0.25.2" "ont-fast5-api==1.2.0" \ "matplotlib>=2.0.0" "pep8==1.7.0" "autopep8==1.2.4" \ "ipython==6.1.0" "pytest==3.1.2" \ "parameterized==0.6.1" "pytest-xdist==1.15.0" $ conda install salmon $ git clone https://github.com/nanoporetech/taiyaki.git $ cd taiyaki $ python setup.py build $ python setup.py install $ conda install -c bioconda bwapy $ conda install -c bioconda pychopper $ conda install -c bioconda pomoxis $ git clone https://github.com/snakemake/snakemake.git $ cd snakemake $ python setup.py build $ python setup.py install $ conda install -c bioconda ont-tombo $ conda install -c bioconda qcat $ conda install -c bioconda wub $ conda install -c bioconda gtfparse $ conda install -c bioconda fastqc $ git clone https://github.com/nanoporetech/megalodon.git $ cd megalodon $ python setup.py build $ python setup.py install $ conda install -c bioconda mako $ conda install -c bioconda drmaa gpustat $ git clone https://github.com/nanoporetech/katuali.git $ cd katuali $ python setup.py build $ python setup.py install $ pip install ont-h5-validator |
'나의일 관련 > Linux' 카테고리의 다른 글
| binutils 관련 오류 기록 (0) | 2019.12.02 |
|---|---|
| nmon gpu 수정 버전 (0) | 2019.11.14 |
| anydesk 간단 설치 및 설정 (0) | 2019.10.31 |
| [Perl 오류] "all" is not exported by the List::Util module (0) | 2019.10.17 |
| python 3 "NameError: name 'file' is not defined " (0) | 2019.05.31 |
