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srgokribb / Rifdock-Total-Setup

Install protocol for Rosetta and Rifdock on CentOS 8 (Red Hat 8.3.1)
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RifDock Setup Protocol for Linux

Least spec to run rifdock

Programs and Resources required to run RifDock

(Bolded programs are directly necessary to build Rifdock)

Notice

Directory Structure

    home/   root/    usr/   opt/

    /root/packages/
                    hdf/     boost-1.65.0/    

    /home/users/local_user/packages/
                     ninja-1.10.2/    re2c-1.0.3/   gcc-6.5.0/    gcc/

    /home/users/local_user/rosetta/
             rosetta_src_release_3.9/     PyRosetta4/      rosetta_src_release_3.13/    rifdock/    scaffolds/    
             psipred/     PatchDock/       ppi_tools/       silent_tools/

    /usr/local/
             bin/   lib/  include/  share/

    /usr/share/Modules/
                    modulefiles/gcc/6.5.0    <-- This "6.5.0" file is the modules file which could be loaded by Environment modules

1. Install HDF5 and Compile Rosetta_3.13 with HDF5

1) Install HDF5 (Ref: https://fossies.org/linux/hdf5/release_docs/INSTALL)

(1) Download HDF5 source file from The HDF5 Group server(https://www.hdfgroup.org/downloads/hdf5) . - Install ver 1.12.1.

(2) Login as administer and make the "packages" directory (This directory will be used to install new libraries, compilers, and etc).

# mkdir packages
# cd packages          // pwd is /root/packages/

(3) Move the downloaded file to the directory you've made (packages/) and unpack the tar file.

# tar -xvzf hdf5-1.12.1-centos8_64.tar.gz

(3) Enter in to the unpacked directory and execute installer file(.sh).

# cd hdf
# ./HDF5-1.12.1-Linux.sh
There will be some explanation and notification for the lisence.
Keep pressing "Enter" to scroll down.
If you see the questions[y/n], type "y" and press "Enter".
# ls
# cd HDF_Group/HDF5/1.12.1
# ls
bin/ include/ lib/ share/

(4) Copy the files to proper directory. /usr/local/bin/ user/local/include/ usr/local/lib/

# cd bin
# cp -r * /usr/local/bin
# cd ../include
# cp -r * /usr/local/include
# cd ../lib
# cp -r * /usr/local/lib

(5) Refresh the shared library cache with "ldconfig".

# ldconfig

(6) Login as local user and set the PATH and LD_LIBRARY_PATH in .bashrc

$ cd ~
$ vi .bashrc

(7) Apply the changed environment.

$ source .bashrc

(8) Check whether $PATH and $LD_LIBRARY_PATH are updated.

$ echo $PATH
$ echo $LD_LIBRARY_PATH

2) Install Rosetta 3.13 and compile with HDF5

(1) Go to Rosetta commons and apply for academic license (https://www.rosettacommons.org/software/license-and-download).

(2) After login in with the ID and password of the license, go to 'Downloads' and enter Rosetta 3.13 - Download Rosetta 3.13.

(3) Download Rosetta 3.13 source (5.2G) file (rosetta_src_3.13_bundle.tgz) and copy the source file to the directory on the Linux computer where the Rosetta 3.13 will be installed (https://www.rosettacommons.org/downloads/academic/3.13/).

(4) Unpack the downloaded file.

 $ tar -xvzf rosetta_src_3.13_bundle.tgz

(5) Move to 'source' directory.

$ cd rosetta_src_release_bundle/main/source

(6) Check 'scons.py' is in the source directory. This file is the software needed to compile Rosetta (already included in the rosetta bundle in main/source directory).

(7) Compile rosetta with HDF5.

$ ./scons.py -j10 mode=release extras=hdf5 rosetta_scripts

(8) Check the compiled result. If the compilation was successfully done, the last sentence of the terminal shows the result like below.

"Install file: "build/src/release/linux/4.18/64/x86/gcc/8/default/rosetta_scripts.default.linuxgccrelease" as "bin/rosetta_scripts.default.linuxgccrelease"
scons: done building targets.

(9) The executable rosetta which is named as "rosetta_scripts.hdf5.linuxgccrelease" will be in /main/source/bin.

2. Install DAIphaBall

(1) DAIphaBall is a part of Rosetta. Move to rosetta_src_release/main/source/external/DAIphaBall.

(2) Type "make" to build DAIphaBall.

$ make

3. Install PyRosetta

(1) Get the license for PyRosetta in Rosetta Commons(https://www.rosettacommons.org/software/license-and-download)

(2) Check the Python version installed on the Linux computer.

$ python --version

(3) Download proper version of PyRosetta4 in PyRosetta server(https://graylab.jhu.edu/download/PyRosetta4/archive/release/)

(4) Move the downloaded file to the directory to install PyRosetta and unzip the file.

$ tar -vjxf PyRosetta4.Release.python36.linux.release-316.tar.bz2

(5) Enter to PyRosetta directory and type

$ cd setup
$ python setup.py install

4. Install PatchDock

(1) Download PatchDock from PatchDock server(https://bioinfo3d.cs.tau.ac.il/PatchDock/).
(2) Unzip the file by
$ unzip patch_dock_download.zip
(3) PatchDock do not require further install process. Read 'README.md' to run PatchDock.

5. Install PsiPred

(3) Unpack the zip file by

$ unzip psipred-master.zip
$ mv psipred-master pripred

(4) Install psipred.

$ cd psipred
$ cd src
$ make
$ make install
$ export PATH=$PATH:/path/to/psipred

(5) Open "runpsipre_single" and revise the path to the "execdir" and "datadir".

$ cd psipred
$ vi runpsipred_single

    #!/bin/tcsh

    # This is a simple script which will carry out all of the basic steps
    # required to make a PSIPRED prediction. Note that it assumes that the
    # following programs are available in the appropriate directories:
    # seq2mtx - PSIPRED V4 program
    # psipred - PSIPRED V4 program
    # psipass2 - PSIPRED V4 program

    # NOTE: Script modified to be more cluster friendly (DTJ April 2008)

    # Where the PSIPRED V4 programs have been installed
    set execdir = ./bin                                               // Change here to /path/to/psipred/bin

    # Where the PSIPRED V4 data files have been  installed
    set datadir = ./data                                              // Change here to /path/to/psipred/data

(6) Test whether the psipred is run

$ cd example
$ ../runpsipred_single example.fasta

6. Set the environment to install and run rifdock (Environment modules, gcc-6.5.0)

1) Install Environment modules

(1) Check whether your computer have Environment Modules.

(2) Download source files of the modules (https://sourceforge.net/projects/modules/files/Modules/modules-4.5.2/).

(3) Install Environment modules (Ref: https://www.admin-magazine.com/HPC/Articles/Environment-Modules).

# cd /usr/local
# mkdir Modules
# mkdir src
# cp modules-4.5.2.tar.gz /usr/local/Modules/src
# tar -xvzf modules-4.5.2.tar.gz
# cd modules-4.5.2
# ./configure
# make
# make install

2) Install GCC 6.5.0

(1) Current GCC verison could be identified by using

 $ gcc --version

(2) Check the kernel version of your system.

 $ uname -r

(3) Download GCC 6.5.0 from GNU server(https://ftp.gnu.org/gnu/gcc/gcc-6.5.0/).

(4) Move the tar.gz file to "packages" directory and unpack the file..

 $ tar -xvzf gcc-6.5.0.tar.gz

(5) Install GCC-6.5.0. on the local directory (Ref: https://gcc.gnu.org/wiki/InstallingGCC).

 $ cd gcc-6.5.0
 $ ./contrib/download_prerequisites
 $ mkdir objdir
 $ cd objdir
 $../configure --prefix=$HOME/path/to/make/GCC-6.5.0 --enable-languages=c,c++,fortran --disable-multilib
 $ make
 $ make install
 $ cd ~ && vi .bashrc

(6) Make "modulefile" for new gcc in /user/share/Modules/modulefiles.

 # cd /usr/share/Modules/modulefiles              //Go to the directory where Modules is installed.
 # mkdir gcc
 # cd gcc
 # vi 6.5.0                                       //This file have basically same format of "modules" file in modulefiles directory.

    #%Module 1.0
    #set    BASEDIR         /opt/[module-info name]
    set     BASEDIR         /path/to/new/gcc
    prepend-path    PATH            ${BASEDIR}/bin
    prepend-path    CPATH           ${BASEDIR}/include
    prepend-path    MANPATH         ${BASEDIR}/share/man
    prepend-path    LD_LIBRARY_PATH ${BASEDIR}/lib64

 # module avail                             //If you check the available modules, then you can see the modulefile of gcc is updated.
 gcc/6.5.0

(7) Login as local user and load new gcc using environment modules.

 $ module load gcc/6.5.0

If you want to automatically load gcc-6.5.0, open .bashrc and add "module load gcc/6.5.0" at the end of the file.

 $ vi .bashrc

    if [ -f /etc/bashrc ]; then
            . /etc/bashrc
    fi

    # User specific environment
    PATH="$HOME/.local/bin:$HOME/bin:$PATH"
    export PATH
    PATH=$PATH:/home/users/srgo/packages/re2c-1.0.3/build:/home/users/srgo/packages/ninja-1.10.2
    export PATH

    # User specific aliases and functions
    module load gcc/6.5.0

(8) Check whether the current GCC version is changed to gcc-6.5.0

$ which gcc
~/path/to/gcc-6.5.0/bin/gcc

7. Install Boost and Ninja to build RifDock

1) Install Boost

Notification: You need to log in as "root" or "administer" to the properly install boost.

(1) Download Boost version 1.65.0 from Boost C++ Library server(https://www.boost.org/users/history/version_1_65_0.html).

(2) Move the downloaded file to the directory to install and unpack the file (Ref: https://valelab4.ucsf.edu/svn/3rdpartypublic/boost/more/getting_started/windows.html).

 # cd /root/
 # mkdir packages
 # cd packages
 # tar -xvzf boost_1_65_0.tar.gz
 # cd boost_1_65_0

(3) Select the location to install the boost by using

 # ./bootstrap.sh --prefix=/path/to/install/boost/

(4) Start installation

 # ./b2 install

2) Load gcc-6.5.0 by modules.

- Important: From here to finishing the building rifdock, keep gcc-6.5.0 mounted on the terminals. See 6.2)-(8)

$ module load gcc/6.5.0
$ which gcc
~/packages/gcc/bin/gcc

3) Install re2c - Needed to run Ninja

(1) Download re2c from downloading site (https://opensuse.pkgs.org/15.3/opensuse-oss-x86_64/re2c-1.0.3-1.18.aarch64.rpm.html).

(2) Install re2c by using following commands (Ref: https://re2c.org/build/build.html).

$ tar -xvzf re2c-1.0.3.tar.gz
$ cd re2c-1.0.3
$ mkdir build
$ cd build
$ ../configure && make && make install

(3) Add the path to executable re2c

$ export PATH=$PATH:/path/to/re2c-1.0.3/build

4) Install Ninja

- In order to build rosetta cxx11_omp, Ninja should be installed and proper PATH of Ninja need to be set.

(1) Download Ninja 1.10.2 from Git-hub(https://github.com/ninja-build/ninja/releases). (Ref:https://github.com/ninja-build/ninja/wiki, https://github.com/ninja-build/ninja)

(2) Install Ninja

 $ tar xvzf- ninja-1.10.2.tar.gz
 $ cd ninja-1.10.2
 $ ./configure.py --bootstrap

(3) Set the proper PATH of Ninja (Necessary)

 $ echo $PATH
 $ export PATH=$PATH:/home/users/local/ninja-1.10.2/
 $ echo $PATH

8. Build Rosetta cxx11_omp and RifDock

1) Build Rosetta 3.9 as cxx11_omp using Ninja

(1) Download Rosetta 3.9 source (2.8G) file (rosetta_src_3.9_bundle.tgz) and copy the source file to the directory where the Rosetta 3.9 will be installed.

(2) Unpack Rosetta

 $ tar -xvzf rosetta_src_3.9_bundle.tgz

(3) Move to main/source directory

 $ cd rosetta_src_release_bundle/main/source

(4) build rosetta cxx11_omp using Ninja(Ref: See 'Extra tools' in https://ninja-build.org/manual.html)

 $ cd rosetta_src_release_bundle/main/source
 $ CXX=/path/to/gcc-6.5.0/bin/g++ CC=/path/to/gcc-6.5.0/bin/gcc ./ninja_build.py cxx11_omp -t rosetta_scripts -remake

2) Build RifDock

(1) Copy rifdock repository and build Rifdock (https://github.com/rifdock/rifdock)

 $ unzip rifdock-master.zip
 $ mv rifdock-master rifdock
 $ cd rifdock
 $ mkdir build
 $ cd build
 $ CXX=/path/to/gcc-6.5.0/bin/g++ CC=/path/to/gcc-6.5.0/bin/gcc CMAKE_ROSETTA_PATH=/Path/to/a/rosetta/main CMAKE_FINAL_ROSETTA_PATH=/Path/to/a/rosetta/main/source/cmake/build_cxx11_omp cmake .. -DCMAKE_BUILD_TYPE=Release
 $ make -j10 rif_dock_test rifgen

2) The unit tests executable file is at:

$ rifdock/build/schemelib/test/test_libscheme

10. Download misc(cao_2021_protocol, scilent_tools, ppi_tools, scaffolds) for RifDock

1) Download cao_2021_protocol

(1) Download design scripts and main pdb files from http://files.ipd.uw.edu/pub/robust_de_novo_design_minibinders_2021/supplemental_files/scripts_and_main_pdbs.tar.gz

(2) Move the file to 'resources' directory and unpack the tar file.

$ cd resources
$ tar -xvzf scripts_and_main_pdbs.tar.gz

(3) Check the files in cao_2021_protocol.

$ cd scripts_and_main_pdbs/supplemental_files/

2) Download scilent_tools and ppi_tools

(1) scilent_tools and ppi_tools are in cao_2021_protocol/github_backup.

$ cd cao_2021_protocol/github_backup/

(2) Add the PATH to scilent_tools to .bashrc (This will be covered in step #11).

3) Download Miniprotein Scaffold Library

(1) Download all the scaffolds from http://files.ipd.uw.edu/pub/robust_de_novo_design_minibinders_2021/supplemental_files/scaffolds.tar.gz

(2) Move the file to 'resources' directory and unpack the tar file.

$ cd resources
$ tar -xvzf scaffolds.tar.gz

(3) Copy scaffold directory to rosetta directory.

$ cp -r supplemental_files/scaffolds ../rosetta

(4) Add the PATH scaffold directory to .bashrc (This will be covered in step #11).

4) Download modular repeat protein database

(1) Download ss_grouped_vall_all.h5 (files.ipd.uw.edu/pub/modular_repeat_protein_2020/ss_grouped_vall_all.h5)

11. Set the proper PATH to all binaries

(1) Move to $HOME and open .bashrc

$cd ~
$vi .bashrc

(2) Set the cursor in the empty line and change to "insert mode" by press "Shift + i" buttons and add the PATH.

from 

    # .bashrc

    # Source global definitions
    if [ -f /etc/bashrc ]; then
            . /etc/bashrc
    fi

    # User specific environment
    PATH="$HOME/.local/bin:$HOME/bin:$PATH"

to

    # .bashrc

    # Source global definitions
    if [ -f /etc/bashrc ]; then
            . /etc/bashrc
    fi

    # User specific environment
    PATH="$HOME/.local/bin:$HOME/bin:$PATH"
    export PATH
    PATH=$PATH:/home/users/srgo/rosetta/rosetta_src_2021.16.61629_bundle/main/source/bin:/home/users/srgo/rosetta/rifdock/build/apps/rosetta:/home/users/srgo/rosetta/scaffolds:/home/users/srgo/rosetta/silent_tools
    export PATH

    LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
    export LD_LIBRARY_PATH

    module load gcc/6.5.0

(3) If you finished the revision, press "ESC" button to exit from "insert mode" and press ":" button and type "wq" and press "Enter" button to save the changes and exit from the file.

    :wq
    (Enter)

(4) Refresh the PATH by "source .bashrc" command and check whether the PATH is sucessfully added.

$ source .bashrc
$ echo $PATH

Good job! You've finished the long journey to install Rifdock.