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Table of Contents | ||
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01.01 Setting Up
Question:
There is a folder called
intro_to_linux
within the/project/arccatrain/
folder.How would you copy this folder into your home folder?
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01.02 Setting Up: Answer(s)
Answer: There are a number of ways…
Code Block |
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# Move to your home folder and copy int this location.
# The “.” marks the current working directory.
[arccanetrain]$ cd
[~]$ cp -r /project/arccanetrain/intro_to_linux/ .
cp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied
[~]$ ls
Desktop Documents Downloads intro_to_linux
# Move into the /project/arccatrain/ folder and copy from there into your home.
# The “~” is short for your home folder.
[~]$ cd /project/arccanetrain/
[arccanetrain]$ cp -r intro_to_linux/ ~
cp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied
[arccanetrain]$ ls ~
Desktop Documents Downloads intro_to_linux
# Why do we see the cp related permission denied?
# -rw------- 1 arcc-t05 arccanetrain 23 Oct 5 07:20 workshop_me.txt
# What happens to this file? It does not get copied. |
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01.03a View the content of files.
Command | Description | ||
cat |
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more |
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head |
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01.03b View the content of files.
Command | Description | ||
tail |
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01.04 Exercises
Code Block |
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[]$ cd ~/intro_to_linux/
[intro_to_linux]$ cat software.csv
[intro_to_linux]$ cat -n software.csv
# Press spacebar to scroll through.
# Press ‘q’ to quit at any time.
[intro_to_linux]$ more software.csv
[intro_to_linux]$ head software.csv
[intro_to_linux]$ head –n 5 software.csv
[intro_to_linux]$ tail software.csv
[intro_to_linux]$ tail –n 5 software.csv |
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01.05 Search for a string within a text file (grep)
Command | Description | ||
grep |
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01.06 Examples: Search a file:
Code Block |
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# Remember: grep is case-sensitive
[intro_to_linux]$ grep NVIDIA software.csv
libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...
libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...
# Nothing is returned.
[intro_to_linux]$ grep nvidia software.csv
[intro_to_linux]$
# Neither of the above picked up “Nvidia”.
[intro_to_linux]$ grep -i NVidia software.csv
compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"...
libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...
libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...
# Ignore the case of the word to search for.
[intro_to_linux]$ grep -n -i NVidia software.csv
145:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"...
152:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...
166:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an... |
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01.07 Examples: Search folders and files:
Code Block |
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[intro_to_linux]$ cd clusters/
[clusters]$ grep -i nvidia *
beartooth.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td>
teton.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td>
[clusters]$ cd ..
[intro_to_linux]$ grep -i nvidia *
grep: clusters: Is a directory
software.csv:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"...
software.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...
software.csv:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...
[intro_to_linux]$ grep -r -i nvidia *
clusters/teton.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td>
clusters/beartooth.html: .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td>
software.csv:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"...
software.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...
software.csv:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an... |
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01.08 Exercises
Code Block |
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# The software.csv file takes the form:
[intro_to_linux]$ head software.csv
Type,Name,Module,Cluster,Description
application,Alphafold,alphafold,"beartooth,teton",AlphaFold...
application,Astral,astral,wildiris,ASTRAL is a tool...
application,Augustus,augustus,beartooth,AUGUSTUS is a program...
application,Avizo,avizo,loren-pre202308,Avizo is a general-purpose...
application,ANGSD,angsd,"beartooth,teton",ANGSD: is a software...
application,ANSYS,ansys,teton,"ANSYS is a general-purpose software... |
Questions:
Which named applications are related to the words “bayes”?
Which files contain reference to IPA?
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01.09 Answers
Code Block |
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[intro_to_linux]$ grep -i bayes software.csv
application,Bayescan,bayescan,beartooth,"BayeScan aims...
application,Beast1,beast1,wildiris,BEAST is a cross-platform program for Bayesian...
application,Beast2,beast2,beartooth,"BEAST 2 is a cross-platform program for Bayesian...
application,Freebayes,freebayes,beartooth,"freebayes is a Bayesian genetic...
application,Jags,jags,"beartooth,teton",Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical...
application,RevBayes,revbayes,wildiris,Bayesian phylogenetic...
application,ROHan,rohan,teton,"ROHan is a Bayesian framework...
application,SourceTracker2,sourcetracker2,"beartooth,teton","SourceTracker, a Bayesian approach...
[intro_to_linux]$ grep -r IPA *
clusters/beartooth.html: .../pages/1893597185/IPA">IPA</a></td>
software.csv:application,IPA,ipa,beartooth,Improved Phased Assembler (IPA) is... |
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