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  • 25d0a112a8 env creation file Ubuntu 2024-11-08 23:13:51 +0000
  • 23eb08a64f Fixed hardcoded paths from testing jscgh 2024-11-01 11:09:41 +1100
  • 7fe0cb6f81 Cleaned up for addition to Proteinfold pipeline jscgh 2024-11-01 10:41:07 +1100
  • e01b10de27 Adding Dronefile JYlag 2024-10-22 18:27:57 -0700
  • 3167908f83 Pushing up all the changes from our Cyrus/Levitate fork JYlag 2024-10-22 18:21:51 -0700
  • df3a0a755f
         Merge 0b87de00c7 into 6c8514053a Andrey Rozenberg 2024-10-22 21:17:26 +0300
  • 0b87de00c7 Fix arguments and paths for make_msa.sh, make make_ss.sh executable alephreish 2024-10-22 12:28:56 +0300
  • 9ef148fa11 Updated to use /app jscgh 2024-10-17 16:52:45 +1100
  • 60c1fb9fc2 Mambaforge deprecated in favour of miniforge jscgh 2024-10-17 16:23:34 +1100
  • 63836b6ec3 Mambaforge deprecated in favour of miniforge jscgh 2024-10-17 16:21:49 +1100
  • c69d920c73 Modified .gitignore Wei-Tse Hsu 2024-10-08 00:23:21 +0100
  • 110002e710
         Merge fe4cefafc1 into 6c8514053a Brandon Frenz 2024-10-07 10:50:48 -0700
  • fe4cefafc1 Merge branch 'run-from-anywhere' of github.com:CyrusBiotechnology/RoseTTAFold-All-Atom into run-from-anywhere Brandon Frenz 2024-10-07 10:50:36 -0700
  • 2fc51e54cc updated the example to remove references to my filesystem paths and provided additional information on how to set the input arguments Brandon Frenz 2024-10-07 10:50:27 -0700
  • 7989d8b4e9 modified: RoseTTAFold-All-Atom.def Mambaforge sunsetted in favour of miniforge jscgh 2024-09-13 14:39:09 +1000
  • e3e6e2bc7b modified: rf2aa/config/inference/base.yaml jscgh 2024-09-02 15:08:58 +1000
  • 8ac5e32885 Added _self_ for hydra compatibility. modified: environment.yaml modified: rf2aa/config/inference/covalent.yaml modified: rf2aa/config/inference/nucleic_acid.yaml modified: rf2aa/config/inference/protein.yaml modified: rf2aa/config/inference/protein_complex_sm.yaml modified: rf2aa/config/inference/protein_na_sm.yaml modified: rf2aa/config/inference/protein_sm.yaml jscgh 2024-09-02 14:46:59 +1000
  • 471f888896 modified: environment.yaml jscgh 2024-09-02 14:19:41 +1000
  • 30ffda1f19 modified: environment.yaml jscgh 2024-09-02 11:53:44 +1000
  • 73d273346a modified: environment.yaml jscgh 2024-09-02 10:00:59 +1000
  • a953992919 Testing dependencies in environment.yaml jscgh 2024-08-30 22:34:07 +1000
  • 833709fc5b modified: environment.yaml jscgh 2024-08-30 22:27:20 +1000
  • 99d36b075f modified: RoseTTAFold-All-Atom-ubuntu.def jscgh 2024-08-30 14:54:28 +1000
  • 436a9c63a8 Merge branch 'dev' of https://github.com/Australian-Structural-Biology-Computing/RoseTTAFold-All-Atom into dev jscgh 2024-08-30 14:07:49 +1000
  • f51fc89c1f t modified: input_prep/make_ss.sh jscgh 2024-08-30 14:07:30 +1000
  • 375a2ef7d4
         Update README.md jscgh 2024-08-30 14:07:07 +1000
  • 005ee45377 modified: RoseTTAFold-All-Atom-ubuntu.def modified: make_msa.sh jscgh 2024-08-30 13:16:58 +1000
  • 8ad64043aa modified: RoseTTAFold-All-Atom.def modified: environment.yaml jscgh 2024-08-30 12:13:49 +1000
  • 8d2fc723c7 modified: environment.yaml jscgh 2024-08-30 11:12:30 +1000
  • 8085a6a97d new file: RoseTTAFold-All-Atom-ubuntu.def modified: RoseTTAFold-All-Atom.def jscgh 2024-08-30 10:59:08 +1000
  • 2d46266cc8 Merge branch 'main' of https://github.com/Australian-Structural-Biology-Computing/RoseTTAFold-All-Atom jscgh 2024-08-27 16:57:11 +1000
  • b55634ed44 modified: RoseTTAFold-All-Atom.def jscgh 2024-08-27 16:56:15 +1000
  • 3b030c41da
         Update README.md jscgh 2024-08-27 16:18:31 +1000
  • 4a38f84663 modified: rf2aa/config/inference/base.yaml jscgh 2024-08-27 15:06:31 +1000
  • cf20754a32 modified: environment.yaml jscgh 2024-08-27 15:01:10 +1000
  • 95ac417e45 modified: RoseTTAFold-All-Atom.def make_msa.sh jscgh 2024-08-27 14:55:02 +1000
  • 40ae0ec7ed modified: input_prep/make_ss.sh jscgh 2024-08-26 12:06:03 +1000
  • 152e18821e modified: RoseTTAFold-All-Atom.def jscgh 2024-08-23 16:57:29 +1000
  • 7c94ae2fc3 modified: RoseTTAFold-All-Atom.def modified: input_prep/make_ss.sh modified: make_msa.sh modified: rf2aa/data/preprocessing.py jscgh 2024-08-23 16:52:20 +1000
  • 026197a05e modified: input_prep/make_ss.sh jscgh 2024-08-23 14:26:42 +1000
  • 17448f9f2f modified: RoseTTAFold-All-Atom.def modified: environment.yaml modified: input_prep/make_ss.sh modified: install_dependencies.sh modified: make_msa.sh jscgh 2024-08-23 13:44:20 +1000
  • c729157c55 modified: RoseTTAFold-All-Atom.def modified: rf2aa/config/inference/base.yaml modified: rf2aa/config/inference/protein.yaml modified: rf2aa/data/preprocessing.py jscgh 2024-08-23 12:08:46 +1000
  • b1d14df81f Removed current working directory indicator in rf2aa/data/preprocessing.py in favour of using PATH variable. jscgh 2024-08-23 11:28:32 +1000
  • 701d1cdacf Fixed modified: README.md jscgh 2024-08-22 14:23:00 +1000
  • 7179216366 new file: RoseTTAFold-All-Atom.def new file: dbs.config modified: input_prep/make_ss.sh modified: make_msa.sh modified: rf2aa/config/inference/base.yaml Added apptainer definition file and db path variables for improved portability. jscgh 2024-08-22 14:20:08 +1000
  • 372d40487b modified: rf2aa/config/inference/base.yaml modified: rf2aa/run_inference.py jscgh 2024-08-13 13:37:59 +1000
  • 607f276d8d modified: make_msa.sh with db params jscgh 2024-08-13 13:18:14 +1000
  • 6a29f0275e Implement batch-mode inference and remove hydra-dependence. benf549 2024-08-06 11:35:17 -0400
  • c6d7ba9712
         Merge 010624bc39 into 6c8514053a Yinying Yao 2024-08-01 10:39:12 +0800
  • 010624bc39 doc: CovalentBond Yinying Yao 2024-08-01 10:37:13 +0800
  • 7ec43e6536
         Merge branch 'main' into run-from-anywhere Sam DeLuca 2024-07-18 09:12:17 -0400
  • 1b327817f3
         Merge bf8822e208 into 6c8514053a Guangfeng Zhou 2024-07-12 07:48:55 +0900
  • 07884921c0
         Merge f6c038563d into 6c8514053a Simon Duerr 2024-07-11 15:45:44 -0700
  • 6c8514053a
         Merge pull request #123 from aolgac/patch-1 main Rohith Krishna 2024-07-11 15:45:37 -0700
  • c1fd92455b
         Merge pull request #127 from clami66/fix_rna Rohith Krishna 2024-06-12 17:44:46 -0700
  • bf8822e208
         Update README.md Guangfeng Zhou 2024-06-12 10:54:12 -0700
  • d1950f2ba6 Added residue replacement to handle protein chemical modifications and NCAAs gfzhou 2024-06-12 10:38:09 -0700
  • a7afaf0b83 fix rna alphabet to avoid one-hot feature crash clami66 2024-06-12 14:31:13 +0200
  • 8de5ed7c41
         ITSD-28112 add placholder for build dependencies such as signalp6 and RFAA_paper_weights.pt Santiago Alvarez Vargas 2024-06-11 21:35:38 -0400
  • ca12a19259
         ITSD-28112 add dockerfile and helper lsf script; also ignore some stuff Santiago Alvarez Vargas 2024-06-11 21:27:08 -0400
  • bc509406fe reverted unnecessary change to the install_dependencies.sh script Brandon Frenz 2024-06-06 15:50:19 -0700
  • 9dcd2e1844 Merge branch 'baker-laboratory-main' into run-from-anywhere Brandon Frenz 2024-06-06 12:27:28 -0700
  • a601bf2fb7 merged my fixes Brandon Frenz 2024-06-06 12:27:15 -0700
  • 8e349bc3c7 created an example directory to run docker jobs Brandon Frenz 2024-06-06 12:12:28 -0700
  • 0aa5f082bc
         Update README.md Abdurrahman OLĞAÇ 2024-06-05 09:42:46 +0300
  • 1543b745c9
         Merge pull request #7 from CyrusBiotechnology/typo-fix Brandon Frenz 2024-05-30 09:49:49 -0700
  • 9f82b2d649 fixed the typo in the database path Brandon Frenz 2024-05-29 16:46:59 -0700
  • 2b46dfb998 forgot to bump version Brandon Frenz 2024-05-29 13:45:19 -0700
  • d061cbe6bd
         Merge pull request #6 from CyrusBiotechnology/docker-cleanup Brandon Frenz 2024-05-29 12:16:27 -0700
  • 36f0482dec more cleanup for the readme BrandonFrenz 2024-05-29 07:27:51 +0000
  • 387779fce8 formating cleanup BrandonFrenz 2024-05-29 07:25:34 +0000
  • cb872066af fix to pathing for the BFD environment variablee in the docker file and error in setting the default path in the make_msa.sh script BrandonFrenz 2024-05-29 07:16:36 +0000
  • da217d60d8 started updating the read.me Brandon Frenz 2024-05-28 13:56:59 -0700
  • 1a867bdcc8
         Merge pull request #5 from CyrusBiotechnology/docker-cleanup Brandon Frenz 2024-05-28 12:13:20 -0700
  • 81a7f879d3 minor cleanup to the Dockerfile Brandon Frenz 2024-05-24 14:54:47 -0700
  • 033691ff1e removed VERSION and drone file Brandon Frenz 2024-05-24 14:50:21 -0700
  • 5a64a77f81
         Merge pull request #4 from CyrusBiotechnology/sync-5-20-2024 Brandon Frenz 2024-05-24 14:20:46 -0700
  • a6384998ed reverted base.yaml to the original BrandonFrenz 2024-05-21 04:22:17 +0000
  • 1b815e6d31 bumped version Brandon Frenz 2024-05-20 12:19:42 -0700
  • f77d2c9b86 removed a comment Brandon Frenz 2024-05-20 11:50:27 -0700
  • 64da0dcf4a changed the make_ss script to only set the BLASTMAT variable if it has not already been set. This provides the freedom to use a blast that hasn't been installed in the main directory Brandon Frenz 2024-05-20 11:45:29 -0700
  • fa35433f8b merged with original Brandon Frenz 2024-05-20 11:34:51 -0700
  • a9f2512cda feat: new covalent bond input YaoYinYing 2024-05-16 20:15:09 +0800
  • 0441fc7982
         Merge pull request #2 from CyrusBiotechnology/cut-version-tag Brandon Frenz 2024-05-14 11:13:44 -0700
  • cd46ed2fb4 bumped version Brandon Frenz 2024-05-14 11:13:02 -0700
  • 91d55ab511 added the cut version tag script Brandon Frenz 2024-05-14 11:12:39 -0700
  • df15c4a1c7
         Merge pull request #1 from CyrusBiotechnology/docker Brandon Frenz 2024-05-14 11:10:53 -0700
  • e2c2fb0653 adding version file JYlag 2024-05-14 08:06:16 -0700
  • ab2fb46469 remove vim rc file JYlag 2024-05-13 19:59:07 -0700
  • 3e85ebc82f remove jsonnet file JYlag 2024-05-13 19:58:24 -0700
  • 000e3b184b small fixes in drone JYlag 2024-05-13 19:57:01 -0700
  • d5f0b7d5b0 changed out the drone file. No idea if this is correct Brandon Frenz 2024-05-13 17:00:06 -0700
  • 16ff5f1c90 fix to the database path. I don't know how this extra b got there but it's probably fine to just leave it. Brandon Frenz 2024-05-13 16:51:17 -0700
  • 105a6fb799 shrunk docker image and fixed issues with psipred and blast BrandonFrenz 2024-05-10 06:02:21 +0000
  • 5e9592b17e got docker micromamba environment working properly and added copied over a drone file and updated it BrandonFrenz 2024-05-03 18:44:43 +0000
  • ee31eac1c3 updated the docker file to run without interactive mode BrandonFrenz 2024-05-03 09:58:44 +0000
  • bf214835d6
         Merge pull request #100 from ToyokoLabs/bugfix33 Rohith Krishna 2024-04-30 08:27:30 -0700
  • d268a4d5f2
         Merge pull request #97 from AlexanderMath/patch-1 Rohith Krishna 2024-04-30 08:25:52 -0700
  • 86b6c4e881 Fixing issue #33 Sebastian Bassi 2024-04-29 10:09:33 -0700
  • d46e8dbd00
         Update README.md AlexanderMath 2024-04-28 12:20:51 +0100