Python Package Install: miniconda

NeranjanV.PereraComputationalBiologyCore

• Example:• HyDe install• https://hybridization-detection.readthedocs.io/installation.html

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

Startaninteractivesessionusingsrun

$srun --mem=1G--partition=general--qos=general--pty bash

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

• Insalling Minicoda https://conda.io/docs/user-guide/install/linux.html• https://conda.io/miniconda.html

• wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

Runthedownloadedbashscriptusing:sh Miniconda2-latest-Linux-x86_64.sh

Thiswillinstallminiconda inyourhomedirectory/home/FCAM/$USER/miniconda2

Onceinstalleditwilladdtheminiconda pathtoyour.bashrc file#addedbyMiniconda2installerexportPATH="/home/FCAM/$USER/miniconda2/bin:$PATH"

Forthischangetobecomeactive,youhavetoopenanewterminal.

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

• Openanewterminal/interactivesession• conda installwillbeactive

• Totesttheconda isactivetype• >conda list

• Updatetheconda• >conda updateconda

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

• Installrequiredpackagesfortheprogramusingconda• >conda installnumpy

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

>conda install-cconda-forgemultiprocess

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

• InstallingHyDe• >git clone https://github.com/pblischak/HyDe.git• >cdHyDe• >pythonsetup.py install

• Installed/home/FCAM/$USER/miniconda2/lib/python2.7/site-packages/phyde-0.4.2-py2.7-linux-x86_64.egg

• Sometimestheremightbeversiondependences• conda search-fcython

• Toinstallaspecificversion• conda installcython==0.25

Institute for Systems Genomics: Computational Biology Core

PythonPackageInstall

Institute for Systems Genomics: Computational Biology Core

XanaduClusterInformation

https://bioinformatics.uconn.edu/resources-and-events/tutorials/