Creating fragment files for Rosetta ab initio

[This guide assumes:
* you know what Rosetta is
* you have admin access to Rosetta files so you can compile it
* you know what ab initio is
* you know where these files are used]

1. Make sure you have the fragment_picker application.

# Testing if the "fragment_picker" file exists in the bin path
test -f <Rosetta_path>/main/source/bin/fragment_picker.* && echo "True"

If it doesn’t exist, you need to compile it.

cd <Rosetta_path>/main/source
./scons.py mode=release extras=cxx11thread fragment_picker -j 32

or for the mpi version:

cd <Rosetta_path>/main/source
./scons.py mode=release extras=mpi fragment_picker -j 32

2. Make sure you have the fragment_tools directory.

# Testing if the "fragment_tools" directory exists in tools path
test -d <Rosetta_path>/main/tools/fragment_tools && echo "True"

If it doesn’t exist, you have to load the tools submodule.

cd <Rosetta-path>/main
git submodule update --init /tools

3. create a script file to run fragment_picker

# If you're using cxx11thread:

export FRAGMENT_PICKER_NUM_CPUS=32
export BLAST_NUM_CPUS=32
export FRAGMENT_PICKER=<Rosetta-path>/main/source/bin/fragment_picker.cxx11thread.linuxgccrelease
<Rosetta-path>/main/tools/fragment_tools/make_fragments.pl -nohoms -verbose <path-to-fasta-file>

# If you're using mpi:

export FRAGMENT_PICKER_NUM_CPUS=0
export BLAST_NUM_CPUS=0
export FRAGMENT_PICKER=<Rosetta-path>/main/source/bin/fragment_picker.mpi.linuxgccrelease
<Rosetta-path>/main/tools/fragment_tools/make_fragments.pl -nohoms -verbose <path-to-fasta-file>

It takes a few hours for the code to run, and at the end, you will have t001_.3mer and t001_.9mer in your working directory.

Note:

This will install external libraries in <Rosetta-path>/main/tools/fragment-tools/, some of which are huge. Make sure you have enough space in your directory, or make symlinks for that directories. Specially for databases .

Acknowledgement:

Thanks to Vikram Mulligan and Rocco Moretti for helping me debug the code.