james-vincent
james-vincent
In version 2.1 from bioconda: xpore-2.1-pyh5e36f6f_0/ in site-packages/xpore: __init__.py:__version__ = "2.0"
## Expected Behavior Fully functioning colab_batch with GPU. ## Current Behavior colabfold_batch: error: unrecognized arguments: --use-gpu-relax ## Steps to Reproduce (for bugs) Install as described for local installation: ./pip install...
Are the databases on https://colabfold.mmseqs.com/ available anywhere else, like AWS? Download speeds are very slow and seem to be limited by at the mmseqs.com end. ## Expected Behavior Download UniRef30...
run_e2e_ver.sh is trying to create cache directory in the RRoseTTAFold install directory. This is not possible on a shared system (HPC). I wonder how others are able to do run...
Relion 5 Job type - PickTomo Key global throws error in pandas. Appears to be coming from: │ 26 │ star = starfile.read(tilt_series_star_file) │ │ ❱ 27 │ global_table =...
**Are you sure this is a bug?** Not sure **Describe the bug** CPU version juicer.sh gets java memory options set like so: Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m Seems to be...
From af2complex/src/alphafold/common/confidence.py pairwise_dist = scipy.spatial.distance.cdist(a, b, metric='euclidean') AttributeError: module 'scipy' has no attribute 'spatial' when running example1.sh. There does not appear to be an import statement for scipy.spatial.
Following installation instructions step by step leads to issue installing two python packages as dependencies: ERROR: pip's dependency resolver does not currently take into account all the packages that are...
Installation instructions do not give specific versions for: pandas pytorch-gpu torchvision These should be specified as tested and known to be working.
The deploy_cluster.sh scripts have hardcoded paths to the src directory required for running the snakemake job. They also have values for time and memory and a few other assumptions like...