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This page will suggest how to use locally and what ARCC infrastructure has provided to make using the provided pipelines more convenient.

Why Locally?

  • We have noticed during testing, that some of the provided scripts appear to require access and write to some internal child folders. This could potentially affect multiple users running concurrently from the same RoseTTAFold folder.

  • The provided pipeline scripts assume they are being running from within the RoseTTAFold install location.

Getting Started

Within your home or project folder, you will need to clone the main git repository and install the csblast and lddt dependencies:

Code Block
# Clone python related scripts.
[@blog2 testing]$ git clone https://github.com/RosettaCommons/RoseTTAFold.git
[@blog2 testing]$ cd RoseTTAFold/
# Install csblast and lddt applications.
[@blog2 RoseTTAFold]$ ./install_dependencies.sh

Why Locally? We have noticed during testing, that some of the provided scripts appear to require access and write to some internal child folders. This could potentially affect multiple users running concurrently from the same RoseTTAFold folder.

Module and sequence and structure database data

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Module and sequence and structure database data
As details on the main RoseTTAFold GitHub page, you can download sequence and structure database data. For convenience we have downloaded this data that currently is >2.2T. 
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 Expand
titleAvailable Folding Related Commands
 Code Block
2to3               env_parallel.ksh     h2ph              h5repack   lzless            perlivp     pydoc3.7           streamzip         x86_64-conda_cos7-linux-gnu-ld
2to3-3.7           env_parallel.mksh    h2xs              h5repart   lzma              perlthanks  python             tabs              x86_64-conda-linux-gnu-ld
acountry           env_parallel.pdksh   h52gif            h5stat     lzmadec           piconv      python3            tclsh             xsubpp
adig               env_parallel.sh      h5c++             h5unjam    lzmainfo          pip         python3.7          tclsh8.6          xz
ahost              env_parallel.tcsh    h5cc              h5watch    lzmore            pip3        python3.7-config   tensorboard       xzcat
captoinfo          env_parallel.zsh     h5clear           idle3      markdown_py       pl2pm       python3.7m         tflite_convert    xzcmp
clear              f2py                 h5copy            idle3.7    matplotlib        pod2html    python3.7m-config  tf_upgrade_v2     xzdec
corelist           f2py3                h5debug           infocmp    ncursesw6-config  pod2man     python3-config     tic               xzdiff
cpan               f2py3.7              h5diff            infotocap  niceload          pod2text    pyvenv             toco              xzegrep
c_rehash           fftwf-wisdom         h5dump            instmodsh  openssl           pod2usage   pyvenv-3.7         toco_from_protos  xzfgrep
enc2xs             fftwl-wisdom         h5fc              json_pp    parallel          podchecker  reset              toe               xzgrep
encguess           fftw-wisdom          h5format_convert  libnetcfg  parcat            protoc      saved_model_cli    tput              xzless
env_parallel       fftw-wisdom-to-conf  h5import          lzcat      parset            prove       sem                tset              xzmore
env_parallel.ash   freeze_graph         h5jam             lzcmp      parsort           ptar        shasum             unlzma            zipdetails
env_parallel.bash  gdbm_dump            h5ls              lzdiff     perl              ptardiff    splain             unxz
env_parallel.csh   gdbm_load            h5mkgrp           lzegrep    perl5.34.0        ptargrep    sql                wheel
env_parallel.dash  gdbmtool             h5perf_serial     lzfgrep    perlbug           pydoc       sqlite3            wish
env_parallel.fish  gif2h5               h5redeploy        lzgrep     perldoc           pydoc3      sqlite3_analyzer   wish8.6
This conda environment provides access to the pyrosetta python package:
 Code Block
[]$ module load miniconda3/23.1.0
[]$ module load rosettafold/1.1.0
[]$ conda activate /apps/u/opt/conda-envs/rosettafold/1.1.0/Folding
(/apps/u/opt/conda-envs/rosettafold/1.1.0/Folding) []$ python
Python 3.7.16 (default, 
lzgrep
Jan 17 2023, 22:20:44)

 perldoc           pydoc3      sqlite3_analyzer   wish8.6
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyrosetta
>>>
Provided pipeline script updates
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 Code Block
CPU="8"  # number of CPUs to use
MEM="64" # max memory (in GB)
The These are then past as arguments into the commands called within the script.
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