Slightly edited version of the chat comment made during the class of April 16,2020
from Zhilin Yang to Everyone: 1:03 PM
A quick question. Do we have to install Ubuntu from Microsoft store? Can I install Ubuntu Desktop from the Ubuntu website?
from Zhilin Yang to Everyone: 1:05 PM
Microsoft store is blocked by IT as well
from Ramiro Iglesias-Bartolome (internal) to Everyone: 1:05 PM
I think it is a great idea to give one more week to catch up!
from Joanna Thomas to Everyone: 1:05 PM
I installed everything ok but wouldn't mind an extra week to practice Unix if others need more time
from Sandeep Gurram to Everyone: 1:06 PM
Same, Its nice to get a little more time to get used to the commands
from Zhilin Yang to Everyone: 1:06 PM
Then can we use our personal PC to finish this class?
from ping xue to Everyone: 1:06 PM
it is ok to stay in Chapter III Unix commend line for one more week. Thanks!
from Monika Mehta (internal) to Everyone: 1:06 PM
Sure, extra week to finish working on unix would be great.
from Mariam Malik (internal) to Everyone: 1:06 PM
would love an extra week. feeling a little rushed at this point.
from Mariam Malik (internal) to Everyone: 1:07 PM
do mac users have to send the decal as well?
from Devon Atkinson to Everyone: 1:07 PM
I was contacted by IT this morning - NCI Frederick had their own install methods working around to install ubuntu
without windows store (not sure how - there was a folder on a server they use) and had to re-add Java.
I was able to do this weeks lesson on my home computer, but I am fine delaying so that others can catch up.
from Monika Mehta (internal) to Everyone: 1:10 PM
My question - how do you get the command prompt back on the terminal once you are in, say the man command for something.
I was also stuck without the command prompt when I entered wc without a file name
from Des to Everyone: 1:11 PM
you can just type "q" to exit a man page;
from Sandeep Gurram to Everyone: 1:11 PM
Also, how do you force cancel a command
from Des to Everyone: 1:12 PM
for getting stuck without the command prompt (i.e. wc without a filename) or
to force cancel a command type and hold the "ctrl" key and press "c"
from ping xue to Everyone: 1:26 PM
cd can only change to one directory at one time?
Verbal answer:
Correct - you can only "exist in a single directory at a time"
from Jeffrey Hanson to Everyone: 1:26 PM
what do -rw-r--r-r stand for?
from Carl McIntosh to Everyone: 1:27 PM
r stands for read permssions
from Carl McIntosh to Everyone: 1:27 PM
w for write
from Monika Mehta (internal) to Everyone: 1:31 PM
can we move files to directory above the current directory?
Verbal answer:
yes you can move files above the current directory by referring to it as "../" e.g. cp file1 file2 ../
from Jerico Santos to Everyone: 1:32 PM
how can you move multiple files into a single directory
Verbal answer:
yes you can move files above the current directory by referring to it as "../" e.g. cp file1 file2 diretory
from Zhilin Yang to Everyone: 1:39 PM
Can I use vim instead of nano?
from Des to Everyone: 1:41 PM
zhilin - yes, you can use vim if you want (i prefer emacs).
from Carl McIntosh to Everyone: 1:39 PM
touch just creates the an empty file with the name
from Zhilin Yang to Everyone: 1:43 PM
is there 'undo' command in unix?
from Carl McIntosh to Everyone: 1:43 PM
no undo after issuing the command
from Monika Mehta (internal) to Everyone: 1:44 PM
how are more and less different from head and tail?
from Carl McIntosh to Everyone: 1:45 PM
less and more allow paging (screen full)
from Carl McIntosh to Everyone: 1:45 PM
less allows paging using the space bar
from Zhilin Yang to Everyone: 1:46 PM
Then if I accidently delete a folder, is there a way to make up? Thanks
from Carl McIntosh to Everyone: 1:46 PM
Yang, not on your local computer, but in biowulf and helix you can recover at some level
rom Zhilin Yang to Everyone: 1:47 PM
Biowulf doesn't backup the files right?
from Carl McIntosh to Everyone: 1:47 PM
on a day, and week level
from Des to Everyone: 1:48 PM
backups on biowulf: https://hpc.nih.gov/storage/backups.html
from Zhilin Yang to Everyone: 1:49 PM
Hi @Des, I read that page before. Most of the data is in the Data directory and that is not backuped
from Des to Everyone: 1:53 PM
Zhilin - yes, not backed up, but it's not deleted until after some time ("Recover files in data directory from snapshot")
from Jerico Santos to Everyone: 1:47 PM
why have a separate command for remove and rmdir?
from Jerico Santos to Everyone: 1:49 PM
can you use rm to remove directory with files in it? maybe that;s the reason why (thought about it just now.)
Verbal answer:
you can use rm to remove a whole directory and its files by using the recursive argument 'rm -r directory'
from Yunlong He to Everyone: 1:52 PM
How to set up the $ sign start on a new line? my $ sign is just flowing my user name and folder name. They are on the same line.
from Carl McIntosh to Everyone: 1:53 PM
Yunlong, PS1="$ "
from Des to Everyone: 1:54 PM
Yunlong -- it's a setting that you can customize in your .bash_profile
from Yunlong He to Everyone: 1:56 PM
Yunlong, PS1="$ "get rid of my user name. how to get it back?
from Carl McIntosh to Everyone: 1:56 PM
Yonlong, open new terminal windo
from Yunlong He to Everyone: 1:57 PM
how to set up .bash_profile?
from Carl McIntosh to Everyone: 1:58 PM
echo "PS1='$ '" >> ~/.bash_profile
from Des to Everyone: 2:00 PM
PS1='\[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '
from Carl McIntosh to Everyone: 2:00 PM
https://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html
from Zhilin Yang to Everyone: 2:07 PM
@Des, thanks for the answer! A following question, is there a way that I can add a warning message to 'rm',
e.g: 'Are you sure you want to delete that file?' Thanks.
from Carl McIntosh to Everyone: 2:07 PM
rm -i
from Des to Everyone: 2:09 PM
If you follow https://www.biostarhandbook.com/computer-setup.html
it will set up your bash environment correctly (i.e. the command prompt display, and the warnings for rm, cp, etc)
from Zhilin Yang to Everyone: 2:10 PM
What about rmdir? There is no '-i' function rt?
from Sandeep Gurram to Everyone: 2:12 PM
I think rmdir only removes empty directories. So you only delete an empty directory
from Monika Mehta (internal) to Everyone: 2:11 PM
what do the x v and f do with the tar command?
Verbal answer:
x means extract
v means verbose (list files are they are extracted)
f indicates the next argument is the name of the tar file to process
from Zhilin Yang to Everyone: 2:18 PM
Do you have a microsoft team for this class?
Verbal answer:
We are exploring how useful Teams will be... more info in the near future
from Des to Everyone: 2:19 PM
Q&A forum: https://btep.ccr.cancer.gov/question/biostar/