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Core NGS Intro class zoom - Shared screen with speaker view
Melanie A. Murphy
40:25
got it.
Nandini Aiyappan
40:42
Yes
Melanie A. Murphy
40:48
No, I cannot see the url in the chat.
Claudia Garcia Jou
40:59
Me neither
Vy Dang
41:00
You can’t see the link?
Melanie A. Murphy
41:08
No, I cannot see the link.
Anna Battenhouse
41:13
https://wikis.utexas.edu/display/CoreNGSTools
Melanie A. Murphy
41:18
Got it. Thanks.
Urbain Weyemi
41:18
Yes
Joanna Henry
01:07:59
me
Denise Furr
01:09:50
I installed Bash from the Windows Subsystem.
Dennis Mishler
01:10:11
I have prior... not sure if currently runnig
Denise Furr
01:10:38
These are a few difficulties.
Denise Furr
01:13:14
can you type the SSH code in the screen?
Amina Zeidan
01:14:06
I get to password and 2 factor authentication, but I keep getting denied
Lydia Tressel
01:16:02
me
Simon Lee
01:16:21
I am also having a trouble
Albert MacKrell
01:16:25
Is it normal to get a message that says "It doesn't appear that you have set up your ssh key"
Md Hassan Uz Zaman
01:16:44
I used the code generated in my Token App, and it worked
Lydia Tressel
01:17:55
I can’t even get through the password portion……it won’t take my password
Vy Dang
01:18:15
Lydia could you try logging in with the tack website first
Zheng Wu
01:18:16
I cant enter the password
Vy Dang
01:18:25
To make sure that your password is the same one
Luciano Cantu
01:18:36
the password wont show when you type it
Vy Dang
01:18:42
Yea that’s normal
Vy Dang
01:18:49
you won’t see anything when you type the password
Lydia Tressel
01:19:16
I can login to the taco website fine……I think it is updating my updated password which should take 30 minutes
Lydia Tressel
01:19:24
tacc
Vy Dang
01:19:25
okay
Luciano Cantu
01:19:38
I was able to login, the TACC token set up with phone number took a few minutes to send a text message
Zheng Wu
01:19:49
got it, thanks
Vy Dang
01:19:50
Okay yay! Let me know when you log in
Vy Dang
01:20:04
is anyone else having trouble?
Vy Dang
01:20:20
Simon did you log in?
Simon Lee
01:20:32
working on it
Urbain Weyemi
01:20:32
For TACC, it seems like you have to be approved first, and it may take a few hours.
Simon Lee
01:20:34
give me a min
Vy Dang
01:21:16
Yes but if you already signed up for the account and Anna approved, shouldn’t be a problem
Vy Dang
01:21:31
That’s why she asked everyone to register long before the course
Riddhiman Garge
01:21:33
I believe everyone should be approved by now, since we asked everyone to signup in advance.
Amina Zeidan
01:21:51
I can log into the website fine as well - I updated my password to see if that would help. The terminal asks for my password 3 times total, so I’m not sure if I’m typing something incorrectly
Vy Dang
01:22:35
Amina my guess is there was some typo. It can be hard when you can’t see what you are typing
Melanie A. Murphy
01:22:40
It is not taking my password.
Lydia Tressel
01:22:41
Amina…..it looks like it takes 30 minutes to update our password
Denise Furr
01:22:47
No
Melanie A. Murphy
01:23:05
I got into the TACC user portal, but in putty it is not taking my password.
Amina Zeidan
01:23:30
Okay I will give it some time and try again - thank you!
Vy Dang
01:23:44
@Melanie, I know it sounds silly but can you type slowly, and make sure you don’t accidentally have the caps lock on?
Vy Dang
01:23:53
I made the same mistake many times before too
Kiley Evans
01:24:09
I am not getting the prompt
Albert MacKrell
01:24:20
ask for help
Denise Furr
01:24:43
I'm into the TACC Portal
Lydia Tressel
01:25:23
me
Melanie A. Murphy
01:25:27
me
Jennifer Tang
01:25:28
me
Melanie A. Murphy
01:26:26
What stage are we at? I was able to log on through the TACC website portion.
Shuge Sun
01:26:45
It normally only takes a few minutes rather than 30 min. So you can keep trying
Lydia Tressel
01:26:51
It worked!!!
Simon Lee
01:28:22
I am in
Vy Dang
01:28:27
awesome
Amina Zeidan
01:29:09
yes
Melanie A. Murphy
01:36:41
Mine actually says "access denied".
Vy Dang
01:37:27
melanie, could you try logging in with a brand new window?
Vy Dang
01:37:44
Its likely that there is a typo in your password
Melanie A. Murphy
01:37:52
I have tried this a couple of times.
Melanie A. Murphy
01:39:23
I did a new window and typed slowly. "access denied".
Vy Dang
01:39:54
and just checking, that same password was good with the TACC user portal?
Melanie A. Murphy
01:40:47
Yes, I am logged in the TACC portal website with the password.
Amina Zeidan
01:41:37
Thank you, I’ll give it some time and try again
Melanie A. Murphy
01:41:48
OK - will wait and try again.
Vy Dang
01:42:02
Fingers crossed
Melanie A. Murphy
01:44:23
So far, still access denied.
Melanie A. Murphy
01:44:57
@Vy Dang - Will be back in just a minute. Need to let the puppy out and then will try again.
Jennifer Tang
01:45:10
Also still getting access denied
Vy Dang
01:45:44
Maybe wait for another 5-10mins
Melanie A. Murphy
01:50:51
Finally in!
Riddhiman Garge
01:51:35
@Melanie That’s great!
Vy Dang
01:52:47
Yay Melanie
Melanie A. Murphy
02:41:56
I am having issue.
Albert MacKrell
02:42:09
same for me and I tried it twice
Chloe Atallah
02:42:17
same here
Kiley Evans
02:42:18
Same
Melanie A. Murphy
02:42:19
same for me. Did the same.
Claudia Garcia Jou
02:42:21
same
Amina Zeidan
02:42:22
Mine is also broken
Melanie A. Murphy
02:42:32
/work/07480/mmurph23/lonestar
Albert MacKrell
02:42:45
echo evaluates without shading
Shuge Sun
02:43:06
same
Melanie A. Murphy
02:43:07
Same, and then I get this: /work/07480/mmurph23/lonestar
Dennis Mishler
02:43:10
Mine is not... but when I made a "test1" it did
Melanie A. Murphy
02:44:32
No.
Amina Zeidan
02:44:41
Mine does not tab complete (MAC)
Claudia Garcia Jou
02:45:04
me neither
Kathryn Thompson
02:45:06
My tab complete doesn’t work
Melanie A. Murphy
02:45:08
It is just giving me a "bing" and nothing.
Albert MacKrell
02:45:10
nope
Eric Young
02:45:21
no
Simon Lee
02:45:24
no
Shuge Sun
02:46:03
same
Kiley Evans
02:47:20
Still red
Chloe Atallah
02:47:22
still broken
Simon Lee
02:47:26
same
Shuge Sun
02:47:28
Still broken
Kiley Evans
02:48:18
It worked!
Melanie A. Murphy
02:48:24
OK, now I have work.
Amina Zeidan
02:48:30
My work file is still red
Md Hassan Uz Zaman
02:49:05
my work file is red as well, is that an issue?
Melanie A. Murphy
02:49:23
My BioITEAM is still red, but now WORK is good.
Claudia Garcia Jou
02:49:57
you have to do mkdir -p work first, then ln -s -f $WORK work
Md Hassan Uz Zaman
02:50:36
yep work and BioITeam are back to cyan
Riddhiman Garge
02:50:59
@Amina is it still broken?
Melanie A. Murphy
02:51:24
The cases are correct.
Alfredo Zuniga
02:51:41
ls
Amina Zeidan
02:51:59
No, I think I just have an extra work file in there that I don’t need, but I can’t remove it. But I do have a cyan coded working work file now
Vy Dang
02:52:23
@amina when you type ls, what do you see?
Amina Zeidan
02:52:53
When I type ls, I see “login1.ls5(33)$ lsBioITeam lonestar scratch work \$WORK”
Vy Dang
02:53:07
okay
Vy Dang
02:53:28
is it \$WORK”
Vy Dang
02:53:32
Or \$WORK
Amina Zeidan
02:54:10
I have \$WORK in red, the others are cyan.
Vy Dang
02:54:20
either way, type: rm ‘\$WORK’
Urbain Weyemi
02:54:20
I am stuck here:
Urbain Weyemi
02:54:22
login2.ls5(16)$ lsscratch worklogin2.ls5(17)$
Amina Zeidan
02:54:33
Yes, it is removed now, thank you!
Melanie A. Murphy
02:54:38
OK - mine are good now. Thank you.
Urbain Weyemi
02:55:14
No. mine is not working
Urbain Weyemi
02:57:14
Not yet
Vy Dang
02:57:33
is anyone else having problem?
Dennis Mishler
02:58:45
basically "shortcuts" from a desktop
Md Hassan Uz Zaman
02:58:47
I have both Lonestar and BioITeam when I do ls- is that what's supposed to happen?
Vy Dang
02:59:07
Remove the Lonestar
Urbain Weyemi
02:59:12
Mine works now
Md Hassan Uz Zaman
02:59:14
gotcha
Vy Dang
02:59:17
okay great
Md Hassan Uz Zaman
02:59:25
yep!
Claudia Garcia Jou
02:59:57
yup
Eduardo Castro
03:00:07
yes
Md Hassan Uz Zaman
03:03:03
"No such file or directory" when I do cd local/bin/ at home
Melanie A. Murphy
03:03:07
login1.ls5(36)$ cdwlogin1.ls5(37)$ cd local/bin/-bash: cd: local/bin/: No such file or directory
Md Hassan Uz Zaman
03:03:16
ah gotcha
Melanie A. Murphy
03:07:59
no, I am trying to catch up.
Kiley Evans
03:08:11
One is broken
Claudia Garcia Jou
03:08:15
Yes
Dennis Mishler
03:08:32
Anna/Vy, is there any commands that will list "common commands" or other basic info [color key, etc...]?
Melanie A. Murphy
03:08:42
Am I supposed to be in the local bin?
Luciano Cantu
03:09:06
there is a manual option to find common commands
Kiley Evans
03:09:23
That fixed it!
Nandini Aiyappan
03:09:29
@Melanie, yes when you try to paste the ln commands you need to be in your bin
Melanie A. Murphy
03:10:14
@Nandini, I have launcher_creator.py and samstat created. But I missed the creating an a folder etc.
Nandini Aiyappan
03:10:59
I have it..Melanie needs to make a directory and move it
Riddhiman Garge
03:11:43
@Dennis the color key is custom depending on OS and how the bashrc file is set up. Anna will get to it I believe.
Claudia Garcia Jou
03:13:04
Same. All good but local is purple.
Vy Dang
03:13:10
Its fine
Vy Dang
03:13:16
Because its a directory
Dennis Mishler
03:20:56
my previous bashrc was green, new one is in white. Was green executable?
Melanie A. Murphy
03:27:13
I completely missed the "singularity" part and not seeing in the wiki. How can I get caught up?
Melanie A. Murphy
03:27:25
Oh, OK.
HAOJIAN LI
03:28:30
Forget to save a copy of .bashrc, does it matter?
HAOJIAN LI
03:29:00
Thanks!
Amina Zeidan
03:29:45
Got it!
Chloe Atallah
03:29:46
all good
Nandini Aiyappan
03:29:47
yes
Claudia Garcia Jou
03:29:47
yes!
Urbain Weyemi
03:30:06
Here is where I am: . .bashrc .cshrc .login scratch work.. BioITeam launcher_creator.py .profile .sshlogin2.ls5(71)$ chmod 600 .bashrclogin2.ls5(72)$
Vy Dang
03:30:32
Yes?
Vy Dang
03:30:51
Are you having any issue?
Claudia Garcia Jou
03:31:02
yes that's fine
Amina Zeidan
03:32:45
Yes
Melanie A. Murphy
03:33:02
Hang on. When I exit, it closes my window and I have to get it going again.
Claudia Garcia Jou
03:33:02
yes
Riddhiman Garge
03:36:23
@Melanie were you able to get back on and notice the differences?
Melanie A. Murphy
03:38:15
Yes.
Melanie A. Murphy
03:38:36
Now behind again...
Melanie A. Murphy
03:40:03
I am behind before this. Where do I start after getting back in and getting to the a/b/c?
Shuge Sun
03:40:26
nothing appears after I typed nano .bashrc
Vy Dang
03:40:38
sHuge where are you
Alfredo Zuniga
03:40:49
Are the class recordings going to be available later today/this week?
Vy Dang
03:40:57
Yes
Shuge Sun
03:40:58
ls5:/work/07439/shuge/lonestar$
Vy Dang
03:41:05
okay do cd ~
Vy Dang
03:41:21
Then ls -la
Shuge Sun
03:41:22
Got it thx!
Vy Dang
03:41:24
see if you have the bash file
Melanie A. Murphy
03:42:34
I am getting this error "If 'For' is not a typo you can use command-not-found to lookup the package that contains it, l ike this:cnf For"
Melanie A. Murphy
03:43:35
ls5:~$ nano .bashrcls5:~$ source .bashrcIf 'For' is not a typo you can use command-not-found to lookup the package that contains it, l ike this:cnf For
Riddhiman Garge
03:49:52
@Alfredo we are recording it. Hopefully we can share it once we figure it out.
Vy Dang
03:51:02
Let us know if anyone is having issue right now
Dennis Mishler
03:55:55
Great job, Anna!
Nandini Aiyappan
03:56:29
Thank you!
Jon Pierce
03:56:38
will each class be recorded so we can try it later?
Vy Dang
03:56:47
yes Im recording it
Vy Dang
03:56:53
It will be posted, time TBD
Vy Dang
03:57:09
Anna will send out an announcement when videos are posted
Eric Young
04:02:22
Thank you everyone! :)
Luciano Cantu
04:02:30
Thank you, have a great rest of your day!
Albert MacKrell
04:02:38
thanks
Chloe Atallah
04:02:43
Thank you!