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AlphaPullDown #39

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boegel opened this issue Oct 7, 2022 · 12 comments
Open

AlphaPullDown #39

boegel opened this issue Oct 7, 2022 · 12 comments
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difficulty: hard software that requires a lot of effort to support new new software priority: high Python site:ugent Software installation request for UGent Tier-2

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boegel commented Oct 7, 2022 •
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@boegel boegel added difficulty: easy software that should be easy to support new new software priority: high Python site:ugent Software installation request for UGent Tier-2 labels Oct 7, 2022
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had to open issue for a dep cctbx-base. It's trying to install stuff into $EBROOTPYTHON
cctbx/cctbx_project#803

deniskristak added a commit that referenced this issue Nov 3, 2022
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progress on #21 finder and #39 alphapulldown
a1e38fd
deniskristak added a commit that referenced this issue Mar 21, 2023
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progress on #39 and #102
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boegel commented Mar 22, 2023

We now have two installation requests for AlphaPullDown

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boegel commented May 15, 2023

Update: we now have three installation requests for AlphaPullDown...

@deniskristak What's the status on this?

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deniskristak commented May 15, 2023 •
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@boegel sorry, I didn't mention this issue in the PR. Here it is, we should be coming to an end: easybuilders/easybuild-easyconfigs#17774

deniskristak added a commit that referenced this issue May 19, 2023
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progress on #39 and cleanup of #106
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boegel commented Jun 5, 2023

@deniskristak PRs merged + software installed, ready for cleanup + closing

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cleaned up

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boegel commented Jun 21, 2023

Re-opening this, since the installation provides on top of fosscuda/2020b and Python 3.8 doesn't work correctly:


I tried to launch an example, but I think there are still some problems with the versioning. More specifically, I am getting a "AttributeError: module 'jax' has no attribute 'Array'" error message when running "from alphafold.model import model". I see that jax 0.2.19 is installed, and on foss-2020b, whereas it ought to be run with 0.3.25 according to AFPD and AF repositories.

It looks like we'll have to figure out the from-source installation of cctbx-base after all...
I'll take a look at that myself, based on https://github.com/conda-forge/cctbx-base-feedstock/blob/main/recipe/build.sh

@boegel boegel reopened this Jun 21, 2023
@boegel boegel assigned boegel and unassigned deniskristak Jun 21, 2023
boegel added a commit that referenced this issue Jun 21, 2023
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add WIP easyconfig for installing cctbx-base from source - dep of Alp…
b0aee46 
…haPulDown (#39)
boegel added a commit that referenced this issue Jun 26, 2023
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progress on cctbx-base (dep for AlphaPullDown #39)
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boegel commented Jun 27, 2023

work-in-progress easyconfig for cctbx-base in https://github.com/vscentrum/vsc-software-stack/blob/wip/39_AlphaPullDown/cctbx-base.eb

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boegel commented Aug 4, 2023

cctbx-base easyconfig now works installing from source, next up is to update the AlphaPulldown easyconfig for foss/2022a...

@boegel boegel added difficulty: hard software that requires a lot of effort to support and removed difficulty: easy software that should be easy to support labels Aug 4, 2023
boegel added a commit that referenced this issue Aug 8, 2023
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add easyconfig file for AlphaPulldown 0.30.7 with foss/2022a (#39)
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boegel commented Aug 8, 2023

PR for AlphaPulldown with foss/2022a: easybuilders/easybuild-easyconfigs#18506

boegel added a commit that referenced this issue Jun 13, 2024
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add WIP easyconfigs for AlphaPulldown 2.0 (beta) #39
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boegel added a commit that referenced this issue Aug 14, 2024
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add easyconfigs for AlphaPulldown 2.0.0b4 (#39)
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boegel commented Aug 14, 2024

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boegel commented Aug 22, 2024

PR for 2023a update:

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