Added pages to OOD

[RobJY]

• OOD Intro
• OOD with Jupyter with Conda & Singularity
• OOD with Matlab
• OOD with RStudio

Still planning on adding the following, but wanted to get some feedback to see if I'm on the right track

• Alphafold2
• Cell-ACDC
• FileZilla
• IGV
• JBrowse Genome Browser
• NGLView Jupyter Notebook
• STATA
• Spark Standalone Cluster
• TeachOpenCADD Notebook

Any suggestions for the pages I've got done?

[s-sajid-ali]

Looks great! Pinging @genericdata for suggestions once you're back from vacation.

[s-sajid-ali]

Now that OOD is getting it's own section, what should we do with this page: https://nyu-rts.github.io/rts-docs-dev/docs/hpc/connecting_to_hpc/ood/ ?

I'm okay with removing it since it'll be duplicated in the new section anyway.

[github-actions]

PR Preview Action v1.6.2
Preview removed because the pull request was closed.
2025-07-22 19:35 UTC

[RobJY]

Sounds good. Thanks @s-sajid-ali !
Yeah, I took some of that information and added it to the intro page here and removed that section from the Setup section in this branch.
Let me know if you see anything later that I should change.

[s-sajid-ali]

One issue that comes up frequently is that users don't know where to look for logs of failed OOD jobs. Unsure if that's a good thing to have or not. It'll mostly help with users debugging their Jupyter issues.

[RobJY]

Yeah, that sounds like a great idea. I'll get that added. Thanks @s-sajid-ali !

[genericdata]

We could put effort towards updating the OOD session cards to say "click here for logs" rather than an external page.

[RobJY]

Sure, that sounds great @genericdata !

I was just writing up in the intro that users could get to the logs by following the Session ID link and then clicking on output.log. I was also going to add instructions for finding the logs from the command line. How does that sound?

[genericdata]

Thats great. I guess it is better to have external documentation as we can link this rather than point to a sub page only visible when running a job.

…

On Wed, Jul 9, 2025, 12:36 PM Robert Young ***@***.***> wrote: *RobJY* left a comment (NYU-RTS/rts-docs#135) <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_NYU-2DRTS_rts-2Ddocs-2Ddev_pull_135-23issuecomment-2D3053308397&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=eJxw9vLxv0bjFu380Lvpew&m=KMAencQkIjxe2ojQFus0VM-rlu1vUK8DZCSfcyuW-dhuH9E_h6G3uPwIrUgpj87v&s=Lj64WbfwCsFiFKcBtif7s9GLo2ulwZet0cttq4WNjF4&e=> Sure, that sounds great @genericdata <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_genericdata&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=eJxw9vLxv0bjFu380Lvpew&m=KMAencQkIjxe2ojQFus0VM-rlu1vUK8DZCSfcyuW-dhuH9E_h6G3uPwIrUgpj87v&s=aJZsRFd-5Ee4XdtpRJWJ9PiONy3Fa2oNa9ptwDsYpqA&e=> ! I was just writing up in the intro that users could get to the logs by following the Session ID link and then clicking on output.log. I was also going to add instructions for finding the logs from the command line. How does that sound? — Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_NYU-2DRTS_rts-2Ddocs-2Ddev_pull_135-23issuecomment-2D3053308397&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=eJxw9vLxv0bjFu380Lvpew&m=KMAencQkIjxe2ojQFus0VM-rlu1vUK8DZCSfcyuW-dhuH9E_h6G3uPwIrUgpj87v&s=Lj64WbfwCsFiFKcBtif7s9GLo2ulwZet0cttq4WNjF4&e=>, or unsubscribe <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AB4RKSDZ4U32NWMGEHDQHDD3HVAKPAVCNFSM6AAAAACBBOEYIKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTANJTGMYDQMZZG4&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=eJxw9vLxv0bjFu380Lvpew&m=KMAencQkIjxe2ojQFus0VM-rlu1vUK8DZCSfcyuW-dhuH9E_h6G3uPwIrUgpj87v&s=YE6wZgiNlAx5niZgTm8vWpDnyGjC1_WDtqJbBnLHDYY&e=> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[RobJY]

I'm all for adding the subpage if you think that would be more intuitive for the users. I just think that whether you add it or not, it's a good idea to have external documentation.

I've pushed a first pass of this added to the intro. Please let me know if you see anything that should be changed. Thanks!

[RobJY]

Hi @s-sajid-ali ,
I saw your Slack message about moving out of dev. Would you like to merge in what I've got so far or wait until there are more pages done?

[s-sajid-ali]

Let's merge this now.