Request: RevBayes v1.3; additional input files

[Ziv Lieberman]

Hello,

I'm very interested in using CIPRES for RevBayes, but the model I am running requires several updates which came in the newest version of Rev. Is there any possibility of providing access to version 1.3.0?

Additionally, I see that currently, only a single input data file can be used. My analysis has a number of inputs besides the molecular alignment, most pertinently a tab-separated data matrix. Is there a way to handle reading these non-alignment files, or is that a current limitation?

Thank you!

-Ziv

[Pfeiffer, Wayne]

Hi Ziv,

I could update the version from 1.2.5 to 1.3.0.

Mark,

* Please let Ziv know whether the current interface will allow what he wants to do or will need to be modified.

Thanks,

Wayne

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[Ziv Lieberman]

Hi Wayne,

Thank you so much! Looking forward to hearing about input options; I will also inquire with the Rev people if they have an alternative approach.

Best,

Ziv

[Miller, Mark]

Hi Ziv,

 

My colleague Wayne Pfeiffer can help update the code, and I can try to be sure the interface can provide what you need.

RevBayres interface at CIPRES does allow multiple data files, as it must to be useful.

Here is a screen shot, which you can investigate at your convenience on the cipres site.

Have a look at the options, and let me know if you need something more.

Note, there is a typo in interface currently,

you can see there are two datafile2.nex prompts, the second one should read datafile3.nex, I am getting that fixed today.

Mark

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[Ziv Lieberman]

Hi Mark,

This looks perfect! I guess I was relying on some old information, so my fault for not keeping up to date! I will let you know if anything else arises, but I think that this should handle all the files that need to be read in (as opposed to just being part of the scriptfile). Thank you both for being so responsive and for all the support!

-Ziv

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[Miller, Mark]

Great. Thanks Liv.

Let me know if anything breaks.

Mark

[Ziv Lieberman]

Hi,

I just wanted to make sure I understand the file naming requirements. Is it true that for 'auxiliary files', the data file itself as uploaded to Cipres can have any name, but the .rev script must refer to them as "./auxfile1.txt" (or whichever number)? For example, I could upload a Newick tree file to Cipres named "mytree.txt", but in the script would use readTrees("./auxfile1.txt") ?

Also, does this same approach apply to the binary datafiles, i.e., I must refer to them in the scrap as "morpho_datafile.nex", or is that just the way they will be renamed by Cipres and they can have whatever name in the data file and the script?

Thank you so much!

-Ziv

[Miller, Mark]

Yes, that is basically correct.

You can upload a file of any name.

However, because of the software design, CIPRES will rename it. This is mandatory.

So you must call the file in the script by the name CIPRES creates.

 

Let me know if I have not answered your question.

[Miller, Mark]

The new version is released now. It uses 1.3 by default. If you clone a job you will want to select the new version.

Mark

On Jun 13, 2025, at 10:17 PM, Miller, Mark <mmi...@sdsc.edu> wrote:



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From: 'Ziv Lieberman' via CIPRES Science Gateway Users <cipres-science...@googlegroups.com>
Sent: Monday, June 9, 2025 6:13 PM
To: CIPRES Science Gateway Users <cipres-science...@googlegroups.com>
Subject: Request: RevBayes v1.3; additional input files

 

Hello,

I'm very interested in using CIPRES for RevBayes, but the model I am running requires several updates which came in the newest version of Rev. Is there any possibility of providing access to version 1.3.0?

Additionally, I see that currently, only a single input data file can be used. My analysis has a number of inputs besides the molecular alignment, most pertinently a tab-separated data matrix. Is there a way to handle reading these non-alignment files, or is that a current limitation?

Thank you!

-Ziv

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[Miller, Mark]

Hi Ziv,

Version 1.3 is released to production now.

If you clone a job, you will want to select 1.3 as the version.

If you create a new job it will be 1.3 by default,

Let me know if you encounter any issues.