I-TASSER and TMHMM Install Guide

This notebook provides a guide to installing I-TASSER and TMHMM in Binder, since these require you to register with your email and cannot be installed beforehand.

import os
import os.path as op

I-TASSER

1. See: http://ssbio.readthedocs.io/en/latest/instructions/itasser.html for instructions on how to obtain the program - follow it up until step 3.
2. Copy and paste the download link below in itasser_download_link
3. Make sure the version number is correct in itasser_version_number
4. Extract the archive
5. Download the I-TASSER library (this will take some time)

Installation will be complete after this. Your paths to execute I-TASSER using ssbio are:

~/software/itasser/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl

with a library directory of

~/software/itasser/ITLIB

# Step 2
itasser_download_link = 'my_download_link'

# Step 3
itasser_version_number = '5.1'

# Step 4
itasser_archive = itasser_download_link.split('/')[-1]
os.mkdir(op.expanduser('~/software/itasser/'))
os.chdir(op.expanduser('~/software/itasser/'))
!wget $itasser_download_link
!tar -jxf $itasser_archive

# Step 5
os.mkdir(op.expanduser('~/software/itasser/ITLIB'))
!./I-TASSER5.1/download_lib.pl -libdir ITLIB

TMHMM

1. See: http://ssbio.readthedocs.io/en/latest/instructions/tmhmm.html for instructions on how to obtain the program - follow it up until step 2
2. Copy and paste the download link below in tmhmm_download_link
3. Run the code below to install tmhmm.

# Step 2
tmhmm_download_link = 'my_download_link'

# Step 3
os.mkdir(op.expanduser('~/software/tmhmm/'))
os.chdir(op.expanduser('~/software/tmhmm/'))
!wget $tmhmm_download_link
!tar -zxf tmhmm-2.0c.Linux.tar.gz

# Replace perl path
os.chdir(op.expanduser('~/software/tmhmm/tmhmm-2.0c/bin'))
!perl -i -pe 's{^#!/usr/local/bin/perl}{#!/usr/bin/perl}' tmhmm
!perl -i -pe 's{^#!/usr/local/bin/perl -w}{#!/usr/bin/perl -w}' tmhmmformat.pl

# Create symbolic links
!ln -s $HOME/software/tmhmm/tmhmm-2.0c/bin/* /srv/venv/bin/