{"type":"doc","content":[{"type":"paragraph","content":[{"text":"Introduction","type":"text","marks":[{"type":"strong"}]},{"text":": Introduce how to work with, view, find and search the content of text files. The workshop is aimed at beginners with basic command-line experience of the Linux file system and will focus on hands-on exercises.","type":"text"}]},{"type":"paragraph","content":[{"text":"Course Goals","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"View the content of text-based files.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Search a file for a string. ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Search for a file/folder by name.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Redirect output from commands and pipe commands together. ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Be very exercise based to allow practice of commands and concepts.","type":"text"}]}]}]},{"type":"rule"},{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"_parentId":{"value":"2134900799"},"style":{"value":"none"}},"macroMetadata":{"macroId":{"value":"620a32a3-f4f8-45f1-a963-410949a2e979"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"0e8f0f06-ae7e-43e9-8c8d-f50b59e7869e"}},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"01 View/Search a File","type":"text"}]},{"type":"paragraph","content":[{"text":"01.01 Setting Up","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Question","type":"text","marks":[{"type":"strong"}]},{"text":":","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"There is a folder called ","type":"text"},{"text":"intro_to_linux","type":"text","marks":[{"type":"code"}]},{"text":" within the ","type":"text"},{"text":"/project/arccatrain/","type":"text","marks":[{"type":"code"}]},{"text":" folder.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How would you copy this folder into your home folder?","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.02 Setting Up: Answer(s)","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Answer","type":"text","marks":[{"type":"strong"}]},{"text":": There are a number of ways…","type":"text"}]},{"type":"codeBlock","content":[{"text":"# Move to your home folder and copy int this location.\n# The “.” marks the current working directory.\n[arccanetrain]$ cd \n[~]$ cp -r /project/arccanetrain/intro_to_linux/ .\ncp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied\n[~]$ ls\nDesktop Documents Downloads intro_to_linux\n\n# Move into the /project/arccatrain/ folder and copy from there into your home.\n# The “~” is short for your home folder.\n[~]$ cd /project/arccanetrain/\n[arccanetrain]$ cp -r intro_to_linux/ ~\ncp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied\n[arccanetrain]$ ls ~\nDesktop Documents Downloads intro_to_linux\n\n# Why do we see the cp related permission denied?\n# -rw------- 1 arcc-t05 arccanetrain 23 Oct 5 07:20 workshop_me.txt\n# What happens to this file? It does not get copied.","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.03a View the content of files.","type":"text","marks":[{"type":"strong"}]}]},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"f7e38a15-7cf3-4070-83d4-329804e541ee"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[117.0]},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[893.0]},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[117.0]},"content":[{"type":"paragraph","content":[{"text":"cat","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[893.0]},"content":[{"type":"codeBlock","content":[{"text":"Usage: cat [OPTION]... [FILE]...\nConcatenate FILE(s) to standard output.\n\n -n, --number\n number all output lines","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#e8ebf5","rowspan":1,"colwidth":[117.0]},"content":[{"type":"paragraph","content":[{"text":"more","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#e8ebf5","rowspan":1,"colwidth":[893.0]},"content":[{"type":"codeBlock","content":[{"text":"more [options] ...\nA file perusal filter for CRT viewing.\nmore is a filter for paging through text one screenful at a time.","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[117.0]},"content":[{"type":"paragraph","content":[{"text":"head","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[893.0]},"content":[{"type":"codeBlock","content":[{"text":"Usage: head [OPTION]... [FILE]...\nPrint the first 10 lines of each FILE to standard output.\n\n -n, --lines=[-]NUM print the first NUM lines instead of the first 10;\n with the leading '-', print all but the last\n NUM lines of each file","type":"text"}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.03b View the content of files.","type":"text","marks":[{"type":"strong"}]}]},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"2a1f59e6-1e1b-422f-b0a4-fbdc8c514cf4"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[117.0]},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[893.0]},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#e8ebf5","rowspan":1,"colwidth":[117.0]},"content":[{"type":"paragraph","content":[{"text":"tail","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#e8ebf5","rowspan":1,"colwidth":[893.0]},"content":[{"type":"codeBlock","content":[{"text":"Usage: tail [OPTION]... [FILE]...\nPrint the last 10 lines of each FILE to standard output.\n\n -f, --follow[={name|descriptor}]\n output appended data as the file grows;\n an absent option argument means 'descriptor’\n\n -n, --lines=[+]NUM output the last NUM lines, instead of the last 10;\n or use -n +NUM to output starting with line NUM","type":"text"}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.04 Exercises","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[]$ cd ~/intro_to_linux/\n[intro_to_linux]$ cat software.csv\n\n[intro_to_linux]$ cat -n software.csv\n\n# Press spacebar to scroll through.\n# Press ‘q’ to quit at any time.\n[intro_to_linux]$ more software.csv\n\n[intro_to_linux]$ head software.csv\n\n[intro_to_linux]$ head –n 5 software.csv\n\n[intro_to_linux]$ tail software.csv\n\n[intro_to_linux]$ tail –n 5 software.csv","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.05 Search for a string within a text file (grep)","type":"text","marks":[{"type":"strong"}]},{"text":" ","type":"text"}]},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"83dccbb7-90e0-4faa-92fa-157a7077df35"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[132.0]},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[878.0]},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[132.0]},"content":[{"type":"paragraph","content":[{"text":"grep","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[878.0]},"content":[{"type":"codeBlock","content":[{"text":"Usage: grep [OPTION]... PATTERN [FILE]...\nSearch for PATTERN in each FILE.\nExample: grep -i 'hello world' menu.h main.c\n...\n -i, --ignore-case ignore case distinctions\n...\n -n, --line-number print line number with output lines\n...\n -r, --recursive like --directories=recurse\n...\n\n# grep is case-sensitive","type":"text"}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.06 Examples: Search a file:","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# Remember: grep is case-sensitive\n[intro_to_linux]$ grep NVIDIA software.csv\nlibraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...\nlibraries and toolkits,TensorRT,,beartooth,\"NVIDIA TensorRT, an...\n\n# Nothing is returned.\n[intro_to_linux]$ grep nvidia software.csv\n[intro_to_linux]$\n\n# Neither of the above picked up “Nvidia”.\n[intro_to_linux]$ grep -i NVidia software.csv\ncompiler,NVidia HPC SDK,nvhpc,\"beartooth,teton\"...\nlibraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...\nlibraries and toolkits,TensorRT,,beartooth,\"NVIDIA TensorRT, an...\n\n# Ignore the case of the word to search for.\n[intro_to_linux]$ grep -n -i NVidia software.csv\n145:compiler,NVidia HPC SDK,nvhpc,\"beartooth,teton\"...\n152:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...\n166:libraries and toolkits,TensorRT,,beartooth,\"NVIDIA TensorRT, an...","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.07 Examples: Search folders and files:","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ cd clusters/\n[clusters]$ grep -i nvidia *\nbeartooth.html: .../788758554/NVidia+HPC+SDK\">NVidia HPC SDK\nteton.html: .../788758554/NVidia+HPC+SDK\">NVidia HPC SDK\n\n[clusters]$ cd ..\n[intro_to_linux]$ grep -i nvidia *\ngrep: clusters: Is a directory\nsoftware.csv:compiler,NVidia HPC SDK,nvhpc,\"beartooth,teton\"...\nsoftware.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...\nsoftware.csv:libraries and toolkits,TensorRT,,beartooth,\"NVIDIA TensorRT, an...\n\n[intro_to_linux]$ grep -r -i nvidia *\nclusters/teton.html: .../788758554/NVidia+HPC+SDK\">NVidia HPC SDK\nclusters/beartooth.html: .../788758554/NVidia+HPC+SDK\">NVidia HPC SDK\nsoftware.csv:compiler,NVidia HPC SDK,nvhpc,\"beartooth,teton\"...\nsoftware.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...\nsoftware.csv:libraries and toolkits,TensorRT,,beartooth,\"NVIDIA TensorRT, an...","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.08 Exercises","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# The software.csv file takes the form:\n[intro_to_linux]$ head software.csv\nType,Name,Module,Cluster,Description\napplication,Alphafold,alphafold,\"beartooth,teton\",AlphaFold...\napplication,Astral,astral,wildiris,ASTRAL is a tool...\napplication,Augustus,augustus,beartooth,AUGUSTUS is a program...\napplication,Avizo,avizo,loren-pre202308,Avizo is a general-purpose...\napplication,ANGSD,angsd,\"beartooth,teton\",ANGSD: is a software...\napplication,ANSYS,ansys,teton,\"ANSYS is a general-purpose software...","type":"text"}]},{"type":"paragraph","content":[{"text":"Questions","type":"text","marks":[{"type":"strong"}]},{"text":":","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Which ","type":"text"},{"text":"named","type":"text","marks":[{"type":"em"}]},{"text":" applications are related to the words “bayes”?","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Which files contain reference to IPA?","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"01.09 Answers","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ grep -i bayes software.csv\napplication,Bayescan,bayescan,beartooth,\"BayeScan aims...\napplication,Beast1,beast1,wildiris,BEAST is a cross-platform program for Bayesian...\napplication,Beast2,beast2,beartooth,\"BEAST 2 is a cross-platform program for Bayesian...\napplication,Freebayes,freebayes,beartooth,\"freebayes is a Bayesian genetic...\napplication,Jags,jags,\"beartooth,teton\",Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical...\napplication,RevBayes,revbayes,wildiris,Bayesian phylogenetic...\napplication,ROHan,rohan,teton,\"ROHan is a Bayesian framework...\napplication,SourceTracker2,sourcetracker2,\"beartooth,teton\",\"SourceTracker, a Bayesian approach...\n\n\n[intro_to_linux]$ grep -r IPA *\nclusters/beartooth.html: .../pages/1893597185/IPA\">IPA\nsoftware.csv:application,IPA,ipa,beartooth,Improved Phased Assembler (IPA) is...","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"02 Search for a File","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.01a Searching for Files: find","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Let us look at a folder with many subfolders and files.","type":"text"}]},{"type":"codeBlock","content":[{"text":"[]$ cd ~/intro_to_linux\n[intro_to_linux]$ ls\nclusters data software.csv\n\n[intro_to_linux]$ ls -R\n.:\nclusters data Intro_to_linux.pdf software.csv vegatables.txt workshop_all.txt workshop_me.txt\n\n./clusters:\nbeartooth.html loren.html teton.html wildiris.html\n\n./data:\n2021 2022 2023 dd.tx\n\n./data/2021:\nApr Nov Sep\n\n./data/2021/Apr:\n20210403.txt 20210427.txt 20210428.txt","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.01b Searching for Files: find","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"./data/2021/Nov:\n20211114.txt 20211115.txt 20211116.txt hello.txt\n\n./data/2021/Sep:\n20210908.txt 20210921.txt\n\n./data/2022:\nDec Feb Hello.csv Jul Jun\n\n./data/2022/Dec:\n20221207.txt 20221220.txt 20221230.txt 20221231.txt\n\n./data/2022/Feb:\n20220203.txt 20220223.txt\n\n./data/2022/Jul:\n20220720.txt 20220722.txt 20220723.TX\n...","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.02 Searching for Files: find","type":"text","marks":[{"type":"strong"}]}]},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"7161da4e-38b8-4ca9-a1bb-9b06a73b658c"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[132.0]},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#4472c4","rowspan":1,"colwidth":[878.0]},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ffffff"}},{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[132.0]},"content":[{"type":"paragraph","content":[{"text":"find","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"background":"#cdd4ea","rowspan":1,"colwidth":[878.0]},"content":[{"type":"codeBlock","content":[{"text":"Usage: find [-H] [-L] [-P] [-Olevel] [-D help|tree|search|stat|rates|opt|exec] [path...] [expression]\n\ndefault path is the current directory; default expression is -print\nexpression may consist of: operators, options, tests, and actions:\n...\nEXPRESSION\n The part of the command line after the list of starting points is the expression. This is a\n kind of query specification describing how we match files and what we do\n...\n TESTS\n ...\n -name pattern\n Base of file name (the path with the leading directories removed) matches shell pattern pattern.\n ...\n -iname pattern\n Like -name, but the match is case insensitive.\n ...","type":"text"}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.03 Examples","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[]$ cd ~/intro_to_linux/\n[intro_to_linux]$ find . -name 20230121.txt\n./data/2023/Jan/20230121.txt\n\n# Check that this file is within the returned location.\n[intro_to_linux]$ ls data/2023/Jan/\n20230102.txt 20230108.txt 20230115.txt 20230121.txt\n\n# Nothing returned – no file exists called “20230120.txt”\n[intro_to_linux]$ find . -name 20230120.txt\n[arcc-t05@blog1 intro_to_linux]$\n\n[intro_to_linux]$ find . -name README.txt\n./data/2021/README.txt\n\n# find is case–sensitive: use –iname option\n[intro_to_linux]$ find . -iname README.txt\n./data/2021/README.txt\n./data/2022/readme.txt\n./data/2023/ReadMe.txt","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.04 Examples","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# Use wildcards to find all files with the postfix .csv:\n[intro_to_linux]$ find . -name \"*.csv\"\n./software.csv\n./data/2022/Hello.csv\n\n# Find any files/folders that contain the string “dec”\n[arcc-t05@blog1 intro_to_linux]$ find . -name \"*dec*\"\n./data/2022/Dec/2022_dec_01.txt\n\n[arcc-t05@blog1 intro_to_linux]$ find . -iname \"*dec*\"\n./data/2022/Dec\n./data/2022/Dec/2022_dec_01.txt\n\n# Find only folders.\n[arcc-t05@blog1 intro_to_linux]$ find . -type d -iname \"*dec*\"\n./data/2022/Dec\n\n# Find only files\n[arcc-t05@blog1 intro_to_linux]$ find . -type f -iname \"*dec*\"\n./data/2022/Dec/2022_dec_01.txt","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.05 Exercises","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Questions","type":"text","marks":[{"type":"strong"}]},{"text":":","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"What do we notice about some of the ","type":"text"},{"text":"find","type":"text","marks":[{"type":"code"}]},{"text":" command options?","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Find any files that contain the string “","type":"text"},{"text":"hello","type":"text","marks":[{"type":"code"}]},{"text":"”, regardless of case, within their filename.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Find any folders or files that contain the string “","type":"text"},{"text":"feb","type":"text","marks":[{"type":"code"}]},{"text":"” regardless of case.","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Can you list only the folders?","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Find any files that have the postfix “","type":"text"},{"text":"tx","type":"text","marks":[{"type":"code"}]},{"text":"” – must be lowercase.","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.06 Answers","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"1: What do we notice about some of the find command options?","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"That some of the single dash options (","type":"text"},{"text":"-name","type":"text","marks":[{"type":"code"}]},{"text":") are similar to long-names and not single letters.","type":"text"}]}]}]},{"type":"paragraph","content":[{"text":"2: Find any files that contain the string “","type":"text"},{"text":"hello","type":"text","marks":[{"type":"code"}]},{"text":"”, regardless of case, within their filename.","type":"text"}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ find . -name \"hello“\n\n[intro_to_linux]$ find . -name \"hello.*\"\n./data/2021/Nov/hello.txt\n\n[intro_to_linux]$ find . -iname \"hello.*\"\n./data/2021/Nov/hello.txt\n./data/2022/Hello.csv\n./data/2023/Mar/HELLO.txt","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.07 Answers","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"3: Find any folders or files that contain the string “","type":"text"},{"text":"feb","type":"text","marks":[{"type":"code"}]},{"text":"” regardless of case.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Can you list only the folders?","type":"text"}]}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ find . -name feb\n./data/2021/feb\n\n[intro_to_linux]$ find . -iname feb\n./data/2021/feb\n./data/2023/Feb\n\n[intro_to_linux]$ find . -iname \"*feb*\"\n./data/2021/feb\n./data/2021/feb/february_01_2021.tx\n./data/2022/February\n./data/2023/Feb\n\n[intro_to_linux]$ find . -type d -iname \"*feb*\"\n./data/2021/feb\n./data/2022/February\n./data/2023/Feb","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.08a Answers","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"4: Find any files that have the postfix “","type":"text"},{"text":"tx","type":"text","marks":[{"type":"code"}]},{"text":"” – must be lowercase.","type":"text"}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ find . -name \"tx\"\n\n[intro_to_linux]$ find . -name \"*tx*\"\n./data/2021/README.txt\n./data/2021/Nov/20211115.txt\n./data/2021/Nov/hello.txt\n./data/2021/Nov/20211114.txt\n…\n\n[intro_to_linux]$ find . -name \"*tx\"\n./data/dd.tx\n./data/2021/feb/february_01_2021.tx\n./data/2023/Jan/texttx\n\n[intro_to_linux]$ find . -name \"*.tx\"\n./data/dd.tx\n./data/2021/feb/february_01_2021.tx","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"02.08a Answers","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# dd.tx is actually a folder.\n# Notices the ’d’ in the long format list.\n[intro_to_linux]$ ls -l data\ntotal 4\ndrwxrwxr-x 6 arcc-t05 arcc-t05 2021\ndrwxrwxr-x 6 arcc-t05 arcc-t05 2022\ndrwxrwxr-x 5 arcc-t05 arcc-t05 2023\ndrwxrwxr-x 2 arcc-t05 arcc-t05 dd.tx\n\n\n[intro_to_linux]$ find . -type f -name \"*.tx\"\n./data/2021/feb/february_01_2021.tx\n\n# We explicitly want lowercase.\n[intro_to_linux]$ find . -type f -iname \"*.tx\"\n./data/2021/feb/february_01_2021.tx\n./data/2022/20220723.TX","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"03 Output Redirection and Pipes","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03 Output Redirection and Pipes","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Redirection of output: > vs >>","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"A ","type":"text"},{"text":"redirect","type":"text","marks":[{"type":"em"}]},{"text":" sends a channel of output to a file.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"You can redirect a file as input to a command using ","type":"text"},{"text":"<","type":"text","marks":[{"type":"code"}]},{"text":" and ","type":"text"},{"text":"<<","type":"text","marks":[{"type":"code"}]},{"text":" (not looked at).","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Using pipe “|’","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"A ","type":"text"},{"text":"pipe","type":"text","marks":[{"type":"em"}]},{"text":" passes ","type":"text"},{"text":"standard output","type":"text","marks":[{"type":"em"}]},{"text":" as the ","type":"text"},{"text":"standard input","type":"text","marks":[{"type":"em"}]},{"text":" to another command","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Examples of the form: ","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"View a text file and pipe to grep.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Cat a list and sort by line.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Sort and then find unique items.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"View folder contents and look for a specifically named name.","type":"text"}]}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.01 Redirection of output: > vs >>","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# Writes out to the command line.\n[intro_to_linux]$ grep -i bayes software.csv\n\n# Redirects the output to a file called apps.txt\n[intro_to_linux]$ grep -i bayes software.csv > apps.txt\n\n[intro_to_linux]$ ls \napps.txt clusters data software.csv\n[intro_to_linux]$ cat apps.txt\n\n# Overwrites any existing file called apps.txt\n[intro_to_linux]$ grep -i IPA software.csv > apps.txt\n[intro_to_linux]$ cat apps.txt\n\n[intro_to_linux]$ rm apps.txt\n\n# Overwrites existing apps.txt\n[intro_to_linux]$ grep -i bayes software.csv > apps.txt\n# Appends to the existing file.\n[intro_to_linux]$ grep -i IPA software.csv >> apps.txt","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.02 Example: Using pipe “|” from a file.","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ cat fruits.txt\nGooseberry\nApple\nApricot\nAvocado\nStrawberry\n...\n\n[intro_to_linux]$ cat fruits.txt | wc -l\n97","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.03 Example continued:","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# The order of items is the same as listed within the fruits.txt file.\n[intro_to_linux]$ cat fruits.txt | grep berry \nGooseberry\nStrawberry\nBilberry\nBlackberry\nMarionberry\nBlueberry\nBoysenberry\nGooseberry\nCloudberry\nElderberry\nGoji berry\nHoneyberry\nJuniper berry\nCranberry\nCranberry\nMarionberry\nGooseberry\nMulberry\nSalmonberry\nHuckleberry\nRaspberry\nSalal berry","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.04 Example continued:","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# Notice the duplicates.\n[intro_to_linux]$ cat fruits.txt | grep berry | sort\nBilberry\nBlackberry\nBlueberry\nBoysenberry\nCloudberry\nCranberry\nCranberry\nElderberry\nGoji berry\nGooseberry\nGooseberry\nGooseberry\nHoneyberry\nHuckleberry\nJuniper berry\nMarionberry\nMarionberry\nMulberry\nRaspberry\nSalal berry\nSalmonberry\nStrawberry","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.05 Example continued:","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"# Duplicates have been removed leaving only the unique names.\n[intro_to_linux]$ cat fruits.txt | grep berry | sort | uniq\nBilberry\nBlackberry\nBlueberry\nBoysenberry\nCloudberry\nCranberry\nElderberry\nGoji berry\nGooseberry\nHoneyberry\nHuckleberry\nJuniper berry\nMarionberry\nMulberry\nRaspberry\nSalal berry\nSalmonberry\nStrawberry\n\n[intro_to_linux]$ cat fruits.txt | grep berry | sort | uniq | wc –l\n18","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.06 Example continued ","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ cat fruits.txt | grep berry | sort | uniq > berries.txt\n[intro_to_linux]$ cat berries.txt\nBilberry\nBlackberry\nBlueberry\nBoysenberry\nCloudberry\nCranberry\nElderberry\nGoji berry\nGooseberry\nHoneyberry\nHuckleberry\nJuniper berry\nMarionberry\nMulberry\nRaspberry\nSalal berry\nSalmonberry\nStrawberry\n\n[intro_to_linux]$ cat berries.txt | wc -l\n18","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.07 Example: Pipe from ls command","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ ls -R\n\n[intro_to_linux]$ ls -R | grep \"Feb\"\nFebruary\n./data/2022/February:\nFeb\n./data/2023/Feb:\n\n[intro_to_linux]$ ls -R | grep -i \"Feb\"\nfeb\n./data/2021/feb:\nfebruary_01_2021.tx\nFebruary\n./data/2022/February:\nFeb\n./data/2023/Feb:","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.08 Exercises","type":"text","marks":[{"type":"strong"}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How does the ","type":"text"},{"text":"wc","type":"text","marks":[{"type":"code"}]},{"text":" command work? What are its options?","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How does the ","type":"text"},{"text":"sort","type":"text","marks":[{"type":"code"}]},{"text":" command work? What are its options?","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How does the ","type":"text"},{"text":"uniq","type":"text","marks":[{"type":"code"}]},{"text":" command work? What are its options?","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How many unique varieties of beans are there in the ","type":"text"},{"text":"vegetables.txt","type":"text","marks":[{"type":"code"}]},{"text":" file?","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"03.09 Answers","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"4: How many unique varieties of beans ae there in the vegetables.txt file?","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How do you deal with “soy beans” vs “Soy Beans”?","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"What options does the ","type":"text"},{"text":"uniq","type":"text","marks":[{"type":"code"}]},{"text":" command provide?","type":"text"}]}]}]},{"type":"codeBlock","content":[{"text":"[intro_to_linux]$ cat vegatables.txt | grep -i beans | sort | uniq -i | wc -l\n12","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"04 More Intermediate Features, Next Steps, Suggestions and Summary","type":"text"}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"04.01a More Intermediate Features","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Environment Variables: Define the behavior of the environment: Try:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"echo $HOME","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"echo $USER","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"echo $SHELL","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"echo $PATH","type":"text","marks":[{"type":"code"}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"File searching/manipulation","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"sed: stream editor for filtering and transforming text","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"gawk: pattern scanning and processing language","type":"text","marks":[{"type":"code"}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Ability to update file permission and ownership: ","type":"text"},{"text":"chmod","type":"text","marks":[{"type":"code"}]},{"text":"/","type":"text"},{"text":"chown","type":"text","marks":[{"type":"code"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"User-case of sharing files/folders.","type":"text"}]}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"04.01b More Intermediate Features","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Aliases in ","type":"text"},{"text":".bashrc","type":"text","marks":[{"type":"code"}]},{"text":".","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Create short-cuts of popular/frequently used commands.","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Text editors: vi/vim/nano","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"vimtutor","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"touch","type":"text","marks":[{"type":"code"}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Remote access with ssh.","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"04.02 Next Steps, Suggestions","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Next Steps on using Linux:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Practicing using Linux online.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Tutorialspoint: ","type":"text"},{"text":"Online Linux Terminal","type":"text","marks":[{"type":"underline"},{"type":"link","attrs":{"href":"https://www.tutorialspoint.com/linux_terminal_online.php"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Best Online Linux Terminals and Online Bash Editors","type":"text","marks":[{"type":"underline"},{"type":"link","attrs":{"href":"https://itsfoss.com/online-linux-terminals/"}}]}]}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Dual boot a Windows machine with Linux.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Run a container image.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Run Linux containers on Windows","type":"text","marks":[{"type":"underline"},{"type":"link","attrs":{"href":"https://ubuntu.com/tutorials/windows-ubuntu-hyperv-containers#1-overview"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to dual-boot Linux and Windows","type":"text","marks":[{"type":"underline"},{"type":"link","attrs":{"href":"https://opensource.com/article/18/5/dual-boot-linux"}}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"UW Researcher? Create a project on the Beartooth cluster with your PI.","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"04.03 Further Trainings: UWYO LinkedIn","type":"text","marks":[{"type":"strong"}]}]},{"type":"mediaSingle","attrs":{"layout":"center","width":375,"widthType":"pixel"},"content":[{"type":"media","attrs":{"__fileSize":48870,"__fileMimeType":"application/octet-stream","width":676,"id":"0d0981ed-2b3a-43e2-a9f3-1c92ec6e460f","collection":"contentId-2134900799","type":"file","__fileName":"zeuPf9AahP77myoUl324vgGcRVXOGW-bIo7NhNzQ69vlCUlN7nWxdQ-nacvordxqJ5VidV4ZZGRJbPgouhIFuhrjhnRKXMQknCEL7Yb0-hFWL4aQhxrZkVNNlYbKW01noEq6kEUAk_npz2LkSoXULA=s2048","height":326},"marks":[{"type":"link","attrs":{"href":"https://www.uwyo.edu/hr/training/linkedin.html"}}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Introduction to Linux","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Learning Linux Command Line","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Linux: Files and Permissions","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Linux: Over and Installation","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Learning Linux Shell Scripting","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"04.04 Request an Account with ARCC","type":"text","marks":[{"type":"strong"}]}]},{"type":"mediaSingle","attrs":{"layout":"center","width":700,"widthType":"pixel"},"content":[{"type":"media","attrs":{"__fileSize":205750,"__fileMimeType":"image/png","width":816,"alt":"image-20240522-200611.png","id":"f33cf30a-a8a9-4ac2-a643-fe3777279d2b","collection":"contentId-2134900799","type":"file","__fileName":"image-20240522-200611.png","height":351}}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Web: ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://www.uwyo.edu/arcc/"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Wiki: ","type":"text"},{"type":"inlineCard","attrs":{"__confluenceMetadata":{"spaceKey":"DOCUMENTAT","isRenamedTitle":true,"linkType":"space"},"url":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT"}},{"text":" ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Portal: ","type":"text"},{"text":"https://arccwiki.atlassian.net/servicedesk/customer/portals","type":"text","marks":[{"type":"underline"},{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/servicedesk/customer/portals"}}]}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"04.05 Summary","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"In this workshop we have:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to search for a string within a file.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to find a file.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to redirect the output of a command into a file.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"How to use pipes to direct the output of one command as the input into another command.","type":"text"}]}]}]},{"type":"paragraph"}],"version":1}