生物信息软件

生物信息类软件可通过 conda, pip 等方法在 π 集群上安装。

安装之前,须先申请计算节点资源(登陆节点禁止大规模编译安装)

$ srun -p small -n 4 --pty /bin/bash

MELT

Manta

Lumpy

Hydra-sv

VariationHunter

GRIDSS

GenomeSTRiP

FermiKit

ERDS

DELLY

CREST

Control-FREEC

CNVnator

CLEVER

BreakDancer

BICseq2

BatVI

BASIL-ANISE

MetaSV

MindTheGap

Mobster

pbsv

Pindel

PRISM

RetroSeq

Sniffles

SV2

SvABA

SVDetect

Wham

gsutil

openslide-python

pandas

cdsapi

STRique

r-rgl

sra-tools

DESeq2

WGCNA

MAKER

AUGUSTUS

DeepGo

km

Requests

MELT安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda melt

Manta安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda manta

Lumpy安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda lumpy-sv

Hydra-sv安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c conda-forge hydra

VariationHunter安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda tardis

GRIDSS安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda gridss

GenomeSTRiP安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda genomestrip

FermiKit安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda fermikit

ERDS安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda erds

DELLY安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda delly

CREST安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda blat
conda install -c bioconda cap3
conda install -c bioconda samtools
conda install -c bioconda perl-bioperl
conda install -c bioconda perl-bio-db-sam
conda install -c imperial-college-research-computing crest

Control-FREEC安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda control-freec

CNVnator安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda -c conda-forge cnvnator

CLEVER安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda clever-toolkit

BreakDancer安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda breakdancer

BICseq2安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda bicseq2-norm

BatVI安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda batvi

BASIL-ANISE安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda anise_basil

MetaSV安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda metasv

MindTheGap安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda mindthegap

Mobster安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda mobster

pbsv安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda pbsv

Pindel安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda pindel

PRISM安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c conda-forge pyprism

RetroSeq安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c hcc retroseq

Sniffles安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda sniffles

SV2安装

完整步骤

module load miniconda3
conda create -n mypy_py27 python=2.7
source activate mypy_py27
conda install -c bioconda sv2

SvABA安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda svaba

SVDetect安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c imperial-college-research-computing svdetect

Wham安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda wham

gsutil安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c conda-forge gsutil

openslide-python安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda openslide-python
conda install libiconv

pandas安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c anaconda pandas

cdsapi安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c conda-forge cdsapi

STRique安装

完整步骤

srun -p small -n 4 --pty /bin/bash
module load miniconda3
conda create -n mypy
source activate mypy
git clone --recursive https://github.com/giesselmann/STRique
cd STRique
pip install -r requirements.txt
python setup.py install

r-rgl安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c r r-rgl

sra-tools安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda sra-tools

DESeq2安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda bioconductor-deseq2

安装完成后可以在 R 中输入 library("DESeq2") 检测是否安装成功

WGCNA安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda r-wgcna

MAKER安装

完整步骤

srun -p small -n 4 --pty /bin/bash
module load miniconda3
conda create -n mypy
source activate mypy
conda install -c bioconda maker

AUGUSTUS安装

完整步骤

srun -p small -n 4 --pty /bin/bash
module load miniconda3
conda create -n mypy
source activate mypy
conda install -c anaconda boost
conda install -c bioconda augustus

DeepGo安装

完整步骤

srun -p small -n 4 --pty /bin/bash
git clone https://github.com/bio-ontology-research-group/deepgo.git
module load miniconda3
conda create -n mypy
source activate mypy
conda install pip
pip install -r requirements.txt

km安装

完整步骤

srun -p small -n 4 --pty /bin/bash
git clone https://github.com/iric-soft/km.git
module load miniconda3
conda create -n mypy
source activate mypy
chmod +x easy_install.sh
./easy_install.sh

Requests安装

完整步骤

module load miniconda3
conda create -n mypy
source activate mypy
conda install -c anaconda requests