57 Commits

Author	SHA1	Message	Date
Kevin Wu	372ec85564	Path fixes	2023-03-09 23:35:17 -08:00
Kevin Wu	403e747368	Multi input support for docker wrapper	2023-03-09 23:02:19 -08:00
Kevin Wu	fe45834ae7	Misc. improvements to file naming	2023-03-09 22:51:02 -08:00
Kevin Wu	de5659e8be	Logging and bugfixes	2023-03-09 17:44:43 -08:00
Kevin Wu	03ef32eb96	Misc. fixes	2023-03-09 16:40:31 -08:00
Kevin Wu	646e1b655e	Ability to speicfy threads in docker	2023-03-09 16:11:06 -08:00
Kevin Wu	9ca513f5e1	Threading updates	2023-03-09 16:02:30 -08:00
Kevin Wu	5de09e00e4	Minor bugfix	2023-03-08 21:25:49 -08:00
Kevin Wu	ccb7d18d19	Add a docker wrapper for gromacs	2023-03-07 22:59:44 -08:00
Kevin Wu	bbcf914050	Performance optimziations	2023-03-07 16:34:22 -08:00
Kevin Wu	868524699f	Docker file for GROMACS	2023-03-07 15:58:45 -08:00
Kevin Wu	ef740c6d39	Speed tweaks	2023-03-07 15:58:32 -08:00
Kevin Wu	dfd6842643	Tweaks to accept files	2023-03-07 15:49:25 -08:00
Kevin Wu	560f0f6b2c	Add mdp files	2023-03-07 15:03:23 -08:00
Kevin Wu	5467ffb9d5	Misc. fixes	2023-03-07 14:52:53 -08:00
Kevin Wu	795cbf7656	Support for gmx binary	2023-03-07 14:50:38 -08:00
Kevin Wu	de5592490d	Reorg files	2023-03-07 14:14:19 -08:00
Kevin Wu	725afc32bd	Add CLI	2023-03-07 14:09:45 -08:00
Kevin Wu	ac83b15a28	Misc. tweaks	2023-03-07 11:44:48 -08:00
Kevin Wu	c3c06eb950	Flesh out gromacs script	2023-03-07 10:45:25 -08:00
Kevin Wu	f3c3c63f1c	Script to do gromacs	2023-02-14 20:00:57 -08:00
Kevin Wu	93f0db0d8a	AF stuffs	2022-11-18 12:59:34 -08:00
Kevin Wu	bc380d5baf	Update omegafold on slurm script	2022-11-17 12:18:04 -08:00
Kevin Wu	80a3457f97	Add a script for running omegafold on slurm	2022-11-17 11:31:03 -08:00
Kevin Wu	de8941bcb6	sherlock AR baseline script	2022-11-07 15:08:51 -08:00
Kevin Wu	e0592b2411	Update README	2022-09-25 23:52:23 -07:00
Kevin Wu	8f3cf1ff0a	Remove statements that caused model collision	2022-09-13 14:34:19 -07:00
Kevin Wu	c45c4cda68	Slurm updates	2022-09-12 17:44:01 -07:00
Kevin Wu	258f702fa3	Reorganize slurm scripts	2022-09-12 17:42:46 -07:00
Kevin Wu	ac5446093d	Add slurm training script	2022-09-12 17:23:01 -07:00
Kevin Wu	3edc076259	Amlt dry runs	2022-09-09 13:35:18 -07:00
Kevin Wu	0b095dbbda	Remove installation of biopython	2022-09-09 10:50:19 -07:00
Kevin Wu	49a6bc349f	Amlt tweak	2022-09-09 09:52:04 -07:00
Kevin Wu	62cf565ed5	Amulet script updates	2022-09-08 14:17:22 -07:00
Kevin Wu	51825e801b	Config updates	2022-09-07 01:38:02 +00:00
Kevin Wu	bd7ffdd7f2	Update yaml	2022-08-30 23:21:46 -07:00
Kevin Wu	f323ccf680	Update amlt yaml	2022-08-30 23:16:19 -07:00
Kevin Wu	f3083bad39	Specify biopython version	2022-08-28 06:35:18 +00:00
Kevin Wu	34ecc9c363	Tar extract file instead of syncing up	2022-08-23 03:18:34 +00:00
Kevin Wu	855b2614d1	Add biopython dependency	2022-08-23 02:09:34 +00:00
Kevin Wu	c2ce89a3de	File cleanup	2022-08-22 17:37:39 +00:00
Kevin Wu	ab22fef1c3	Typo fixes	2022-08-19 20:36:30 +00:00
Kevin Wu	aad06dd86a	Update amlt and config files for full run	2022-08-19 20:33:07 +00:00
Kevin Wu	2405d0147b	Update toy tests for dual GPU	2022-08-17 20:29:43 +00:00
Kevin Wu	04d6f83e9d	Add astropy dependency	2022-08-17 18:49:54 +00:00
Kevin Wu	eb4c008789	Add mpl scatter density dependency	2022-08-17 18:41:58 +00:00
Kevin Wu	ee5cf029cf	Amulet yaml without conda	2022-08-17 17:15:51 +00:00
Kevin Wu	2bf70a5a93	Amulet script for toy run	2022-08-16 21:04:28 +00:00
Kevin Wu	33bd83dcfe	More amulet	2022-08-16 18:15:05 +00:00
Kevin Wu	251ae9f5d3	Amulet update	2022-08-16 18:14:16 +00:00