Member Site › Forums › Rosetta 3 › Rosetta 3 – Build/Install › Compiling rosetta to include rosetta_scripts_jd3
- This topic has 8 replies, 2 voices, and was last updated 2 years, 10 months ago by
Anonymous.
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August 24, 2021 at 6:41 am #3827
Anonymous
Hi,
I’ve currently installed rosetta3 on aws cloud vm under ubuntu OS (Ubuntu 20.04.2 LTS).
I try to use a protocol from Khersonsky et al. 2018 (PMID: 30270109).
In order to do so, a rosetta_scripts_jd3.default.linuxgccrelease file is needed.
However, I did not find such file under $ROSETTA/main/source/bin/
My rosetta version is: rosetta_src_2021.16.61629_bundle
I’ve compiled it with: ./scons.py -j8 mode=release bin
How to compile/install rosetta in order for the rosetta_scripts_jd3.default.linuxgccrelease to be available ?
Thanks in advance,
Oz
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August 24, 2021 at 12:07 pm #15994
Anonymous
The application is not yet public, and probably shouldn’t have been used for that paper. In the coming weeks, the app will be moved to public and released with the associated paper.
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August 25, 2021 at 10:06 pm #15995
Anonymous
Thanks you jadolfbr.
I will check again for newer installtion in a couple of weeks.
Still, or maybe I’m confusing, but in Khersonsky et al. Mol. Cell 2018 (PMID: 30270109) in the sup. pdf (also in this link: https://www.cell.com/cms/10.1016/j.molcel.2018.08.033/attachment/aa873311-1ddc-466a-accf-723dba2789b4/mmc4)
they wrote:
” rosetta_scripts_jd3.default.linuxgccrelease @mutate.flags -in:file:job_definition_file job.xml “
Thanks again,
Oz
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August 25, 2021 at 11:50 pm #15996
Anonymous
They did. They had access to the developer source and at the time, this was my pilot app and not released. However, they would have been able to do what they did with more manual scripts or pyrosetta. Still, it probably shouldn’t have been used – especially as at that time ithe code had just got written.
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August 26, 2021 at 10:46 am #15997
Anonymous
Thanks for the clarifications
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October 1, 2021 at 10:55 pm #16031
Anonymous
This is now in Rosetta and should be available in the next weekly release.
Documentation is here: https://new.rosettacommons.org/docs/latest/RosettaScripts-JD3
Reference is here: https://www.biorxiv.org/content/10.1101/2021.09.27.462000v2
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October 7, 2021 at 12:24 pm #16034
Anonymous
Thanks, this is very helpful.
Will the next version include binaries ?
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October 7, 2021 at 12:49 pm #16036
Anonymous
Yes, next weekly release will include the app.
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November 9, 2021 at 10:32 am #16059
Anonymous
Hi jadolfbr,
Do you know when the new weekly realese with the j3 is about to be published ?
I checked this url (that is the most recent link I found on this section of the website) :
https://www.rosettacommons.org/downloads/academic/2021/wk38/
and I couldn’t find the jd3 script among the bin files.
Thanks,
Oz
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