General Cyverse Information

Laura Condon, Jan 2019

Creating and Account and Getting Access:

In order to upload data, you need to create a Cyverse account and be given permissions by Laura. Provide the username of your account and the e-mail you used to create the account (your UA e-mail) to Laura.

Logging in:

De.cyverse.org

Our Server:

  • You can find under Community Data/avra
  • From command line: /iplant/home/shared/avra

GUI file transferring with cyberduck

https://cyberduck-quickstart.readthedocs.io/en/latest/#

Setting up irods so you can do command line transfers:

  1. Sign up for a cyverse account: https://user.cyverse.org/register
  2. Install icommands so you can use irods
  3. Initialize irods by typing iinit and then putting in your user information following part two of the link on step 2

**Command line transfers with irods: **

First initialize irods like this:

* _iinit_
* [data.cyverse.org](http://data.cyverse.org/)
* Port: 1247
* User: yourusername
* Zone: iplant
* Then enter your cyverse password

To upload:

  • cd to the local directory with the data you want to transfer
  • Then ‘icd’ to the location on Cyverse where you want to put the data
    • icd /iplant/home/shared/avra #for avra
    • icd /iplant/home/username #for your Cyverse home directory (note this is small and not where you should be storing things)
  • iput -vP “filename"
  • To batch upload: iput -K -P -b -r -T folder-where-you-want-files-on-cyverse/
    • If you icd to where you want to put your files on cyverse then you simply need to put a period after the iput command’
      1. iput -K -P -b -r -T .
    • -K “This causes iCommands to verify that transferred files weren't corrupted during the transfer by comparing the Checksums computed before and after the transfer.”
    • -P provides progress feedback
    • -b allows for bulk uploads
    • -r includes a folder or directory
    • -T renews socket connection every 10 min
  • If its a tar file you can extract it on Cyverse like this:

To Download:

  • Basically the same thing but with iget instead of iput

Links with irods info:

icommands help: https://wiki.cyverse.org/wiki/display/DS/Using+iCommands

Setting up irods commands for R:

  • You should be able to run i commands in R using the system function. e.g. system(‘ils')
  • If you get a warning saying command not found even though you have them installed you probably need to modify your R path so it can find them. To check this echo $PATH on command line and compare with system(‘echo $PATH) within R (You can also check this with Sys.getevn() to see everything or Sys.getenv("PATH”) to just see the path in R)
  • To fix you can set a new path appending the icommands to your current path like this: Sys.setenv(PATH='/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/icommands')
  • Then you also need to add the plugin: Sys.setenv(IRODS_PLUGINS_HOME="/Applications/icommands/plugins/")
  • Then check the path and check that it worked using getenv and testing an icommand.
  • NOTE: If you get an irods host error at this point its probably because you haven’t run iiint
  • PERMANENT Fix: If you don’t want to have to add the Sys.setenv to every script then do the following:
    • vi ~/.Rprofile (just make the file if you don’t have one)
    • Add the following lines:
      • Sys.setenv(PATH='/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/icommands')
      • Sys.setenv(IRODS_PLUGINS_HOME="/Applications/icommands/plugins/")
    • Note this will permanently set your environment variables

Running an Analysis on Atmospheres

Steps to run on the Cyverse Rstudio App

  • Login: de.cyverse.org
  • Click on Apps - Search for ‘Rstudio’
  • Select ‘rocker-geospatial-3.5.0’ # you can also add it to your favorites
  • Give your analysis a name - you don’t have to change anything though if you don’t want
  • Click ‘Launch Analysis’
  • Then if you click on ‘Analyses’ on the left you should see the job you just launched it will say ‘running’ but its probably still initializing.
  • Click on the arrow next to its name to open the tab and you will see it launching your application.
  • You will need to login to Cyverse and then R studio the first time it launches.For Rstudio the username and password are both rstudio
  • Once you are in Rstudio - click on the terminal window
    1. iinit
    2. Checkout the GitHub repo
  • Once you have done this you will see ‘CONUS1_Warming’ in your files tab
  • Go to R scripts and click on the Rmd file you can run from here