Hi, will the username and password be given later to connect to workshop.colorado.edu?. Thanks

hi @Jeff Lessem (he/him), just wanted to check if I needed to do anything about this: I wrote the "success" file and did ls, but unlike the example in your email, my "Desktop" is a hidden directory: workshop_45:~> touch success workshop-45:~> ls R success workshop-45:~> ls -la total 57 drwxr-xr-x 12 katerz97 students 16 Jun 1 10:53 . drwxr-xr-x 297 root root 301 May 27 14:17 .. drwxr-xr-x 2 katerz97 students 3 Sep 27 2013 .Desktop -rw-r--r-- 1 katerz97 students 220 May 12 2008 .bash_logout -rw-r--r-- 1 katerz97 students 3526 May 15 2017 .bashrc drwxr-xr-x 3 katerz97 students 3 May 6 11:25 .cache drwxr-xr-x 5 katerz97 students 5 Jun 1 10:50 .config drwx------ 3 katerz97 students 3 Sep 27 2013 .gconf drwx------ 3 katerz97 students 3 Jun 1 10:48 .gnupg drwx------ 3 katerz97 students 3 Sep 27 2013 .kde drwxr-xr-x 3 katerz97 students 3 Jun 1 10:50 .local drwx------ 5 katerz97 students 5 Feb 13 2019 .mozilla -rw-r--r-- 1 katerz97 students 807 Apr 17 2019 .profile drwx------ 2 katerz97 students 5 May 6 11:25 .ssh drwxr-xr-x 3 katerz97 students 3 Jun 1 10:50 R -rw-r--r-- 1 katerz97 students 0 Jun 1 10:53 success

That's fine. I found the Desktop directory was a bit confusing, so I made it a hidden file. I could have deleted it, but some of the faculty who already had accounts had things in there, and it was easier to script renaming it, than to check it for things I didn't put there before deleting it.

*Thread Reply:* I was coming here to ask the same question! Thanks!

*Thread Reply:* I'm glad people are paying attention!

Hi jeff I tried to create the file called success and when I typed ls i got the output "R success" instead of "Desktop success"

*Thread Reply:* Yes, that's fine. I deleted the Desktop directory because some people were confused by it, and it doesn't make any sense when working remotely.

Hi Jeff, I haven't had any issues with the "success" file, but I've noticed that others have had R in the ls output as well. However, I do not - is this problematic?

*Thread Reply:* No, it doesn't matter. The R directory will get automatically created by Rstudio when you login to it for the first time.

*Thread Reply:* Okay, thank you!

Hi Jeff, how can I save R scripts that I wrote on RStudio server locally? I can't find my directory through "save as"...

*Thread Reply:* Yes, it is tricky to find in "save as", the easiest way is to find the ... square near the top right. Click on that, and then in the dialog box put just a ~ (the tilde) and then hit OK, and it will change the directory shown in save as to be your home directory.

*Thread Reply:* That is if you have navigated to someplace else first, then you have to do the ~ thing to get back to your home directory.

*Thread Reply:* Thanks! I am also wondering how I can save everything that is in my personal directory on the server to my local computer?

*Thread Reply:* Yes, will have to download it. The easiest thing is to use a file transfer utility that understands scp or sftp. If you are using bitvise, then that is the file browser window that opens with a terminal window. There are other options depending on what operating system you're on, such as filezilla, cyberduck, winscp

The week after the class, I'll also offer a zip file of everything in your home directory, so you can download it all at once.

I am running the R studio locally in my system and cannot open the dat files. Should I download any package in R? Thanks

*Thread Reply:* I replied in <#C01TLU7JAQK|anonymous-question-box> just leaving a link to it here for reference https://boulder-workshop.slack.com/archives/C01TLU7JAQK/p1623079302004700?thread_ts=1623079037.004600&cid=C01TLU7JAQK

} Jeff Lessem (https://boulder-workshop.slack.com/team/U01N0M6SKL3)

<p>If you are running rstudio local to you, then you will have to download the files from the <code>/faculty/conor</code> to your computer and open them there.</p> <p>There are lots of R packages that have been loaded. If you run <code>ls /usr/local/lib/R/site-library/</code> on the server you will see the many that I have loaded.</p> <p>For tomorrow, you will need OpenMX, umx, MASS, psych, and maybe some others.</p> <p>That's why I generally recommend people use the hosted Rstudio, so they don't have to worry about that stuff during the practicals. Of course, you will need to worry about it for doing this stuff later on your own.</p>

Original URL: https://boulder-workshop.slack.com/archives/C01TLU7JAQK/p1623079302004700?thread_ts=1623079037.004600&amp;cid=C01TLU7JAQK

From a thread in <b>#anonymous-question-box</b>

Back when we received our usernames and instructions to log onto the cluster, I changed my password to a go-to one to make it easier to remember. I am trying to log on now w/ that pwd and my permission is denied. I tried the original pwd as well, in case I had not properly changed it after all but that also won't work. Is there a way to have my password for the cluster reset? Apologies!

*Thread Reply:* I'll change it back to the original one

*Thread Reply:* OK, it is reset. Let me know if you're still having trouble.

*Thread Reply:* thank you! I will just keep that email saved and use that pwd moving forward.

*Thread Reply:* it's still not working -- but I think it may be a username issue -- it is populating with my local university username (csheerin@workshop.colorado.edu) and not my workshop one (chriss29)

*Thread Reply:* Yes, that will cause a problem. use ssh <a href="mailto:chriss29@workshop.colorado.edu">chriss29@workshop.colorado.edu</a>

*Thread Reply:* ugh -- so sorry -- I was in auto pilot and clearly putting in the wrong username automatically! that did the trick. THANK YOU

*Thread Reply:* No problem, glad it's working.

Hi Jeff, I tried logging into Rstudio today for the practical and after logging in I got a blank loading screen. I tried logging in before the course and everything worked perfectly. My internet connection seems to be working just fine too. Could you please help me find out what happened? Thanks 😃

*Thread Reply:* This can usually be fixed by deleting the files in your workshop account in .local/share/rstudio I've don that, so you should be able to use RStudio now. I'm not exactly sure what is happening with the files that make it so you can't login.

*Thread Reply:* Let me know if it still isn't working.

*Thread Reply:* It's working now! Thanks a lot

*Thread Reply:* I think I am having the same issue. what command do I use to delete the files that you mentioned?

*Thread Reply:* now it's working, not sure why :)

Hi @Jeff Lessem (he/him) I had some issues yesterday getting the tutorial data downloaded yesterday. Could you post instructions on where to find the relevant directories so I can get them before the session today. (Apologies if this is already posted somewhere and I've missed it). Thanks

*Thread Reply:* Liz posted it in the #general channel, but it is easy to miss: https://boulder-workshop.slack.com/archives/C01NQAHGKAL/p1623150726265900

} Elizabeth Prom-Wormley (https://boulder-workshop.slack.com/team/U01UAESHT4Y)

<p>If you need additional instructions. There are two ways you can copy files to your personal folder: METHOD 1 1) copy files into your personal folder using your ssh client. You can use the following code in ssh client to copy everything into your folder: mkdir day2 cd day2 cp -r /faculty/hmaes/2021/day2/** ./   2) go to Rstudio on the server and open/work from the folder where your newly copied data/code are located.   METHOD 2 1) Open up your SSH client. Then copy/paste, and run the line below. (shell script written by Tim Poterba [thank you Tim!] and edited for today). Then open your RStudio on the server and begin work. sh ~elizabeth/day2_prac.sh</p>

Original URL: https://boulder-workshop.slack.com/archives/C01NQAHGKAL/p1623150726265900

Thread in <b>#general</b>

Thank you!

I am trying to copy the day 2 practical and am getting cp: no match. workshop-35:~> mkdir day2 workshop-35:~> cd day2 workshop-35:~/day2> cp /faculty/hmaes/2021/day2/./ cp: No match. workshop-35:~/day2> cp/faculty/hmaes/2021/day2/./ cp/faculty/hmaes/2021/day2/./: No match. workshop-35:~/day2> cp /faculty/hmaes/Boulder2021/day2/./ cp: No match. workshop-35:~/day2> cp /faculty/hmaes/2021/day2/./ cp: No match. workshop-35:~/day2**>

*Thread Reply: try cp -r /faculty/hmaes/2021/day2/*./

*Thread Reply:* That didn't work, unfortunately

*Thread Reply:* Fixed!

*Thread Reply:* Glad it's working. It looks like it was a missing space cp -r /faculty/hmaes/2021/day2/** ./ an extra long space in the line, to show where it should be. (They system doesn't care if you have 1 space or several)

*Thread Reply:* The (hopefully not mansplainy) explanation: cp <source> <destination>

im having trouble copying the day 3 data into my file- I keep getting the error object 'cp' not found

*Thread Reply:* It looks like you're trying to copy it from within R. The copying needs to be down from an SSH terminal. Let me know if you need help getting logged in with SSH.

*Thread Reply:* thank you! that is correct!

I just copied the syntax from the google doc

> mkdir day3 Error: unexpected symbol in "mkdir day3" > cd day3 Error: unexpected symbol in "cd day3" > cp -r /faculty/katrina/2021/QC/ . Error: object 'cp' not found > cp -r /faculty/lucia/2021/GWAS/ . Error: object 'cp' not found >

@Jeff Lessem (he/him)

Hi faculty, the absolute beginners (like me) are plodding through the Zoom practicals very slowly compared to everyone else. Is there a way of streaming us, or at least putting all the beginners in the same Zoom room together after the main session finishes?

*Thread Reply:* Yes, I think we can ask around at the end of the session and move you to the same room . Good idea, thanks for suggesting!

Hi! I am trying to copy over the files to my directory for today's practical and am receiving the error message below: cp: cannot access 'GenomicSEM_practical/.Rproj.user/233136F9/viewer-cache': Permission denied I copied the code as provided - is there a way for me to be able to copy things over?

*Thread Reply:* Hey Sarah, @Michel Nivard mentioned this during Session A. This file is not necessary for the practical. Everything else should copy over just fine.

*Thread Reply:* Thank you @Peter Tanksley!

I tried to install the GenomicSEM package on my RStudio and encountered a warning saying to download Rtools before proceeding. I followed the instructions listed here https://cran.r-project.org/bin/windows/Rtools/ (I created a text document in my downloads file) but when I run Sys.which(“make”) I got the following output: > Sys.which(“make”) make  “”   How can I properly set up the path to my Rtools installation? Thank you!

Hi @Jeff Lessem (he/him), In the past when I attended, I received an email a few weeks (or days) after with all my notes and scripts from the workshop. Is that the plan for this year's workshop as well? If not, what would be the best way to download the files to my own computer/server? Sorry, if this was already stated; I may have missed it. Thanks again for helping make sure everything ran smoothly from start to finish!

*Thread Reply:* Yes, I'm preparing that right now! I need to wait for the B session to complete, but I expect to send out the email with your unique file link this weekend, or early next week.

The general file list for the course just went up at https://www.colorado.edu/ibg/international-workshop/2021-international-statistical-genetics-workshop/workshop-2021-file

*Thread Reply:* Awesome! You all are just amazing! Thanks again! (Just feeling like I can't say thank you enough and I know how much work is also involved on the back end... and it really just ran sooooo smoothly for a virtual workshop!)