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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 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.
Step1:  I-TASSER
See
Step2:  TMHMM
See
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Python Code:
import os
import os.path as op
Explanation: 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.
End of explanation
# 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
Explanation: I-TASSER
See: http://ssbio.readthedocs.io/en/latest/instructions/itasser.html for instructions on how to obtain the program - follow it up until step 3.
Copy and paste the download link below in itasser_download_link
Make sure the version number is correct in itasser_version_number
Extract the archive
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
End of explanation
# 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/
Explanation: TMHMM
See: http://ssbio.readthedocs.io/en/latest/instructions/tmhmm.html for instructions on how to obtain the program - follow it up until step 2
Copy and paste the download link below in tmhmm_download_link
Run the code below to install tmhmm.
End of explanation
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