Question: How to run Autodock 4 , using CONDA environment on server
0
gravatar for tushar19221
12 weeks ago by
tushar192210 wrote:

Hey I am new to Virtual Screening. To learn this I had started with tutorial named “Using AutoDock 4 for Virtual Screening”. ( http://autodock.scripps.edu/faqs-help/tutorial/using-autodock4-for-virtual-screening )

I was able to replicate the results (UPTO exercise 11) on my local machine.

Now I am trying to replicate the section named “Using the TSRI cluster: garibaldi” on my college server.

I do not have sudo rights in my college server.
So what I did was: 1) Installed CONDA on the server. I made a virtual environment there. 2) Installed autodock, autodock Vina, autodocktools, mgltools on CONDA environment. 3) Then I downloaded the file “submit4.py” and kept it in the path (here in the bin file of my CONDA environment) (I had changed the default path in the script) (attaching the script of submit4.py). 4) When I am launching my jobs. There I am getting this error - “sh: 7: qsub:Permission denied”. [1]

I had traced this problem back to 32nd line of the submit4.py script. The line is- “ qsub -l cput=23:00:00 -l nodes=1:ppn=1 -l walltime=23:30:00 -l mem=512mb %s.j >> %s ”


so my questions are:

Question1: Am I doing this right , means do setting up conda like this works for virtual screening ?

Question2: How can I modify the script submit4.py) according to my server requirements?

The script for submit4.py:

#!/usr/bin/env python
#
# Usage: submit4.py stem ndlgs

import sys, posix, time

path = "/home/tushar19221/anaconda3/envs/tushar_env/bin/autodock4"

stem = sys.argv[1]
ndlgs = int(sys.argv[2])
ndlg_start = 1
if (len(sys.argv) == 4):
  ndlg_start = int(sys.argv[3])

cwd = posix.getcwd()

created = time.time()
jobIDsName = """%s.%.2f.jobIDs""" % (stem, created)
command = """touch %s\n""" % (jobIDsName,)
posix.system(command)

for i in xrange(ndlg_start, (ndlg_start + ndlgs)):
    #
    jobname = """%s.%03d""" % (stem, i)
    #
    command = """echo "ulimit -s unlimited
echo SHELL is $SHELL
echo PATH is $PATH
cd %s
/home/tushar19221/anaconda3/envs/tushar_env/bin/autodock4 -p %s.dpf -l %s.dlg" > %s.j
chmod +x %s.j
qsub -l cput=23:00:00 -l nodes=1:ppn=1 -l walltime=23:30:00 -l mem=512mb  %s.j >> %s
""" % (cwd, path, stem, jobname, jobname, jobname, jobIDsName)
    #
    posix.system(command)
    #
    # next i

command = """echo "Job %s was launched on %d processors with these 
job_identifiers:"

cat %s\n""" % (stem, ndlgs, jobIDsName,)
posix.system(command)

ADD COMMENTlink modified 8 weeks ago by Biostar ♦♦ 20 • written 12 weeks ago by tushar192210
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