Could the website be a wiki? Or can I get edit permission?

Hi. The CellProfiler download links on the website are partially outdated and broken, i.e. broken links are “source” and “Linux 32bit” and “Linux 64bit”, the “Windows 64bit” link targets an old version of CellProfiler, and the “Linux 64bit” link targets the newest Windows CellProfiler :smile: . There is also a link to Java, but it is not explicitly linking to the JDK, so users might be confused to install the JRE (which is not sufficient to execute CellProfiler). I’m also not sure if the CentOS link on is still valid, at least the link does not open in a web browser which is usually not a good sign. It makes it also hard to tell which version it would link to.

Cutting a long story short, its almost impossible to install CellProfiler due to broken links.

I would like to help fix the situation, but I lack edit permissions. Could the website be replaced with a wiki? Or could I get edit permissions? I’ll try not to break things :smiley:

You are so gracious to offer to help out! We appreciate you keeping an eye on things and specifying what’s broken. We’ve known about these issues but are a little swamped with a single software engineer right now - thankfully a second will be joining us who can help sort things out, given the rest of us don’t know how.

My suspicion is that you’d need to be a Broad employee to get behind the firewall to have permissions to fix this, but I’ve asked @allen_goodman to be sure.

Actually the website is all on Github here:

@emmenlau would just need to be added as a “collaborator” and given proper permissions:

Though fixing some of these would be a bigger issue! The Windows build is linked to the continuous integration server and maybe it’s fixed now but it was broken, but you would certainly need to be behind the Broad firewall to do that. The Linux links are broken and perhaps @emmenlau could help with the source links, but again, the builds would best be linked directly to any build integration which @allen_goodman is best to answer.

I could do this, but I’ll leave this to current members to authorize! :slight_smile:

P.S. @LeeKamentsky tried hard to find permanent links to the proper Java needed for install, but oddly this proved difficult (impossible?)

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Working on permissions now…

Ok, @emmenlau has write privileges there so can push to the website’s repo! Great solution.

Great, thanks for the very quick response! My first changes are online, and the download links work again. I took the liberty to make a few other changes here and there, but I haven’t finished the layout of the downloads page, so please bare with me while I will try to finish my changes :slight_smile:
P.S. @David_Logan you are right that its impossible to link to Java downloads directly. But I’ve changed the link from JRE to JDK, and reiterated on the downloads page that the JDK is the required download - I hope it will help at least some of the users.

I’m fairly certain for the prebuilt versions only the JRE is necessary, not the JDK. If you’re building your own JDK is required.

Also don’t see any Java link/instructions atm but you may be editing it now.

Thats interesting! I am pretty certain I tried installing CellProfiler on Windows 8, while having the JRE installed, and it would not even install. I downloaded and installed JDK and it worked after that. I also just emailed with a friend who could not run 2.2.0 on Mac, and she had to install JDK too to get it running. I will retry with Windows to be sure…

It’s possible, I’m running roughly a billion versions of CP at the moment between 3 Windows computers (all installed at different times obviously) so I may misremember, but that to the best of my recollection is true for Windows.

I take everything back! Its very curious, but I can not reproduce the behavior now. I took the snapshot of the VM only after installing the JDK, so I can not reproduce the exact same situation anymore. And now it seems to work with just the JRE installed. This is quite curious because I only downloaded and installed the JDK on top of JRE in order to get CellProfiler installed. Well, maybe it was a one-time problem, or a mistake on my side. Thanks!

About the website: The download page follows a different design than the other pages, i.e. it is missing the header and footer. I like the new design, but it would be nice if all pages followed the same convention, and the missing header breaks the navigation. Can somebody advise how I could to continue? Is this part of a larger design change? Or just an artifact that I could fix by re-adding the header and footer?

Thanks for your work @emmenlau.

  • I was also not 100% sure, but like @bcimini though that JRE and not JDK was the only requirement (someday that will go away too)
  • The releases webpage reorganization was a quick fix by @allen_goodman at the time back in April I think, and is anticipating a fuller update. So if I recall correctly, we didn’t have a strong preference to try and force the releases page to have the same web format, though there are obvious reasons to keep them all uniform. I think @Anne_Carpenter, @daviddao, and perhaps @allen_goodman can provide the best current thoughts on the website reorg.
  • Yeah, I really don’t understand why Oracle doesn’t have a permanent link to JDE/JDKs!

Indeed, we’ve had a new site design settled since the beginning of the year but ran into troubles deploying it. It’s on the agenda (like a lot of other things!) So it’s pointless to make the release page prettier. But correct/useful sure would be nice!

Good, thanks for the quick feedback!

  • I will refrain from updating the website design, and focus on the content! On a side note: I like the information in your github wiki a lot, and at some point I found it hard to know when to look on the website and when in the wiki. My personal preference would be a united wiki at (with all content in one place). But that’s just me! :blush:
  • About the JDK/JRE, I have a new finding: my colleague tested CellProfiler 2.2.0 on Mac OS X, and found that (at least) on 10.11.5 it is required to have the JDK installed, JRE seems not sufficient. Any Mac users around that can confirm?

Great job emmenlau!
Also I’m very glad to hear that CellProfiler team is about to expand :slight_smile:

One more thing:
Beta (2.3.0) for Windows introduce itself as CellProfiler 2.2.0 rc2. If it is not really 2.3.0 then in my opinion it should be removed.

Thanks fafafft. I’ve removed the link until there is a “true” Beta 2.3.0 release :slight_smile: