Last updated: 2022-07-25
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Knit directory:
SISG2022_Association_Mapping/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | e54c1bf | Joelle Mbatchou | 2022-07-24 | Build site. |
| html | 660617e | Joelle Mbatchou | 2022-07-22 | Build site. |
| html | 7453eb7 | Joelle Mbatchou | 2022-07-22 | Build site. |
| html | 819830c | Joelle Mbatchou | 2022-07-22 | Build site. |
| Rmd | 8ab3b45 | Joelle Mbatchou | 2022-07-22 | add more info for windows users |
| html | 4612d53 | Joelle Mbatchou | 2022-07-20 | Build site. |
| Rmd | c5eb893 | Joelle Mbatchou | 2022-07-20 | edit guide |
| html | d6a44cb | Joelle Mbatchou | 2022-07-20 | Build site. |
| Rmd | 08e3c3a | Joelle Mbatchou | 2022-07-20 | guide for server |
We will be using an online server to run the module exercises.
To get setup:
ssh <username>@<server_address><default_password>passwd after you login(Note: the server adress and default password were posted on the Slack channel)
Please make sure you are able to access the server prior to us starting the class on Monday July 25th. Let us know on Slack if you have any issues with the above steps.
If you run into issues accessing the server, we recommend Mobaxterm with X11 forwarding or Windows Subsystem for Linux as an SSH client to access the server.
We have loaded data sets needed for the class exercises onto the
server at /data/SISG2022M15/data/. We recommend to create a
symbolic link in your home directory (i.e. default directory when you
ssh into the server) to this folder for easier use during the module. To
do that, run the following command in the terminal from your home
directory:
ln -s /data/SISG2022M15/data/ dataYou should now see the class datasets by just using
ls data/ (note that you only have read access to these
files).
Template R code is available for some of the exercises to get your
started; these are available in /data/SISG2022M15/code/. We
recommend you copy this folder over to your home directory so you will
be able to modify the files when you try out the exercises.
To do that, run the following command in the terminal from your home directory:
cp -r /data/SISG2022M15/code/ code/You should now see the R files using ls code/ (note that
you have read/write access to these files).
We have started a RStudio server so you can start a Rstudio session from your web browser which will run on the online server. To connect your browser to the online server:
ssh -fNL 1235:localhost:8787 <username>@<server_address>After you have entered your password, the ssh session should close.
localhost:1235. You
should be re-directed to the RStudio login page where you can enter your
username/password (same credentials you use when ssh-ing into the
server).Once logged in, the working directory will be your home directory so
you can easily access the template R scripts in code/ as
well as the class datasets in data/.
You can use pkill ssh to terminate the ssh session (so
you won’t be able to access RStudio server from your browser anymore);
until then it will remain accessible unless you restart your computer
(or log out).
We strongly encourage you to use this when doing the class exercises so it will be easier to run scripts from RStudio, load datasets as well as visualize plots.
ssh -XY <username>@<server_address>data/ and
code/ subdirectories, respectively).
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.0
loaded via a namespace (and not attached):
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[5] pillar_1.7.0 later_1.3.0 git2r_0.30.1 tools_3.6.1
[9] getPass_0.2-2 digest_0.6.25 jsonlite_1.7.2 evaluate_0.15
[13] tibble_3.1.6 lifecycle_1.0.1 pkgconfig_2.0.3 rlang_1.0.4
[17] cli_3.1.1 rstudioapi_0.13 yaml_2.2.1 xfun_0.31
[21] fastmap_1.1.0 httr_1.4.3 stringr_1.4.0 knitr_1.39
[25] sass_0.4.0 fs_1.5.2 vctrs_0.3.8 rprojroot_2.0.3
[29] glue_1.6.1 R6_2.4.1 processx_3.5.3 fansi_0.4.1
[33] rmarkdown_2.14 callr_3.7.0 magrittr_1.5 whisker_0.4
[37] ps_1.7.0 promises_1.2.0.1 htmltools_0.5.2 ellipsis_0.3.2
[41] httpuv_1.6.5 utf8_1.1.4 stringi_1.4.6 crayon_1.3.4