1 Introduction to Python LING 5200 Computational Corpus Linguistics Martha Palmer.
Data Therapy Python Package - Computational Biology Core
Transcript of Data Therapy Python Package - Computational Biology Core
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Python Package Install: miniconda
NeranjanV.PereraComputationalBiologyCore
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• Example:• HyDe install• https://hybridization-detection.readthedocs.io/installation.html
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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Startaninteractivesessionusingsrun
$srun --mem=1G--partition=general--qos=general--pty bash
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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• Insalling Minicoda https://conda.io/docs/user-guide/install/linux.html• https://conda.io/miniconda.html
• wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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Runthedownloadedbashscriptusing:sh Miniconda2-latest-Linux-x86_64.sh
Thiswillinstallminiconda inyourhomedirectory/home/FCAM/$USER/miniconda2
Onceinstalleditwilladdtheminiconda pathtoyour.bashrc file#addedbyMiniconda2installerexportPATH="/home/FCAM/$USER/miniconda2/bin:$PATH"
Forthischangetobecomeactive,youhavetoopenanewterminal.
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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• Openanewterminal/interactivesession• conda installwillbeactive
• Totesttheconda isactivetype• >conda list
• Updatetheconda• >conda updateconda
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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• Installrequiredpackagesfortheprogramusingconda• >conda installnumpy
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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>conda install-cconda-forgemultiprocess
Institute for Systems Genomics: Computational Biology Core
PythonPackageInstall
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• 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
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Institute for Systems Genomics: Computational Biology Core
XanaduClusterInformation
https://bioinformatics.uconn.edu/resources-and-events/tutorials/