alphafold_on_euler merge requestshttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests2023-09-28T09:22:37Zhttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/16Update file README.md -- remove LSF2023-09-28T09:22:37ZnmarouninaUpdate file README.md -- remove LSFhttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/15Moving to AF2.3.1, full SLURM2023-09-12T17:11:59ZnmarouninaMoving to AF2.3.1, full SLURMScript has been modified for the new installation of Alphafold 2.3.1. Additionally, all of the LSF references has been removed. Finally, the resource recommendations accounts for the tests that has been made on AF2.3.1Script has been modified for the new installation of Alphafold 2.3.1. Additionally, all of the LSF references has been removed. Finally, the resource recommendations accounts for the tests that has been made on AF2.3.1https://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/13Corrected the task allocation syntax in the output2023-01-20T12:13:04ZnmarouninaCorrected the task allocation syntax in the outputThere was a SLURM syntax mistake in the previous commit (--ntask has been used without the "=" sign). I correct it hereThere was a SLURM syntax mistake in the previous commit (--ntask has been used without the "=" sign). I correct it herehttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/12fixed Slurm submission options2023-01-19T13:06:25Zruedsimofixed Slurm submission optionshttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/10Added the Ubiquitin fasta file2022-12-05T14:18:59ZnmarouninaAdded the Ubiquitin fasta fileProvided for testing the script and Alphafold on the clusterProvided for testing the script and Alphafold on the clusterhttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/9Updated the script's usage with the batch system option2022-12-05T14:09:53ZnmarouninaUpdated the script's usage with the batch system optionhttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/8Created an option that generates the script to submit the alphafold job with ...2022-11-01T07:47:21ZnmarouninaCreated an option that generates the script to submit the alphafold job with SLURMnmarouninanmarouninahttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/7Integrate postprocessing script2022-09-05T11:57:00ZbrgerharIntegrate postprocessing scriptCo-authored-by: ruedsimo <simon.ruedisser@biol.ethz.ch>Co-authored-by: ruedsimo <simon.ruedisser@biol.ethz.ch>brgerharbrgerharhttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/6Revert "Adjusted the syntax of the if conditions for the options"2022-09-05T10:05:53ZnmarouninaRevert "Adjusted the syntax of the if conditions for the options"This reverts commit c451181bab79c8b70e436316dcadc0acf96a6b30
The suggested syntax was wrongThis reverts commit c451181bab79c8b70e436316dcadc0acf96a6b30
The suggested syntax was wrongbrgerharbrgerharhttps://gitlab.ethz.ch/sis/alphafold_on_euler/-/merge_requests/5Miscellaneous fixes & improvements2022-08-16T05:58:19ZjjaenesMiscellaneous fixes & improvements- Fix --skip_minimization
- Support fastas with multi-line sequences
- Add `--reduced_dbs` to run AF2 with `—db_preset=reduced_dbs`
- Add `--reduced_rsync` to skip copying large results files (MSAs, pickles) from the compute nodes
- Plac...- Fix --skip_minimization
- Support fastas with multi-line sequences
- Add `--reduced_dbs` to run AF2 with `—db_preset=reduced_dbs`
- Add `--reduced_rsync` to skip copying large results files (MSAs, pickles) from the compute nodes
- Place AF2 output & log files relative to the working directory (`-w`)