Usage-env00-base.md

The 'base' environment is the default environment of conda, usually not be used, ALWAYS activate your own environment.

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FYI, this page introduces the common/basic command usages for beginners (suitable for any MacOS or LinuxOS, including any installed conda environments).

Updated on 2023-06-16

Usage description

Usage text

  # annotation line
  (environment) ~/location$ command line
  
  # for any environments and any locations
  (*) $ command line
  
  # '$' in Linux = '%' in Mac, means the current location

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Basic Usage

For more or detailed explanations, please refer here (English or Japanese or Chinese) or Google it.

## Change directory/location
# change to a specific folder
(*) $ cd path/to/your/folder/ 
# back to the upper directory
(*) $ cd ..
# back to home directory (~)
(*) $ cd

## Check the current directory/location
(*) $ pwd

## List 
# list contents for the current directory
(*) $ ls
# list contents for a specific directory
(*) $ ls path/to/directory/
# list contents with all details
(*) $ ls -l

## Create a new directory named 'NAME'
(*) $ mkdir NAME

## Copy
# copy one or more files
(*) $ cp path/to/file1 (file2 file3) path/to/save/directory/
# copy folder
(*) $ cp -r /path/to/folder path/to/save/directory/

## Move/rename
# move file/folder to other location (give path if needed)
(*) $ mv file1 path/to/save/directory/
# rename the file/folder (give path if needed)
(*) $ mv old_name new_name

# change extensions (.fa => .fna)
(*) $ for f in *fa; do mv -- "$f" "${f%.fa}.fna"; done 


## Remove/Delete
# delete files (give path if needed)
(*) $ rm file1 file2 file3
# delete folders (give path if needed)
(*) $ rm -r folder1 folder2 folder3

## Clean
# clean the screen (delete all contents on the current screen)
(*) $ clear

zip and unzip

# unzip the .gz file
(*) $ gzip file.gz
# unzip current all .gz files ('./' means current directory )
(*) $ gzip ./*.gz

Conda Related (Homepage)

# check conda version
(*) $ conda --version

# list all environments 
(*) $ conda-env list
or
(*) $ conda info --envs 

# enter a sepcific environment (ex: 'NAME')
(*) $ conda activate NAME
(NAME) $ 

# quit current environment
(NAME) $ conda deactivate
(base) $

# list all installed tools in the located environment ('NAME')
(NAME) $ conda list

# install/uninstall packages in the current environmnet
(NAME) $ conda install xxx
(NAME) $ conda uninstall xxx

Remote upload/download

## for file
# upload to remote
(*) $ scp /path/to/local/file user_name@IP_address:/path/to/directory/
# dowload to local
(*) $ scp user_name@IP_address:/path/to/file/ /path/to/local/directory/ 

## for folder
# upload to remote
(*) $ scp -r /path/to/local/folder/ user_name@IP_address:/path/to/directory/
# dowload to local
(*) $ scp -r user_name@IP_address:/path/to/folder/ /path/to/local/directory/ 

'user_name@IP_address' : same as your connect/login info

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More General Usages

grant permission to the file

# 755 permission (777: all permission)
(*) $ sudo chmod 755 file

check running processes :'top'

# Top command
(*) $ top

cut the files: 'cut'

# 
(*) $ 

split the files: 'split'

# 
(*) $ 

sort the files: 'sort'

# 
(*) $ 

text filter1 simple: 'grep'

# 
(*) $ 

text filter2 stronger: 'sed'

# 
(*) $