#!/usr/bin/env python
# coding: utf-8

# In[1]:


get_ipython().run_cell_magic('bash', '', 'echo "TODAY\'S DATE:"\ndate\necho "------------"\necho ""\nlsb_release -a\necho ""\necho "------------"\necho "HOSTNAME: "; hostname \necho ""\necho "------------"\necho "Computer Specs:"\necho ""\nlscpu\necho ""\necho "------------"\necho ""\necho "Memory Specs"\necho ""\nfree -mh\n')


# In[2]:


get_ipython().run_cell_magic('bash', '', 'mkdir /home/sam/analyses/20180103_oly_pbjelly\n')


# In[3]:


ls /home/sam/analyses/20180103_oly_pbjelly/


# In[4]:


get_ipython().run_cell_magic('bash', '', 'cp /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml /home/sam/analyses/20180103_oly_pbjelly/\n')


# In[5]:


get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[6]:


get_ipython().run_cell_magic('bash', '', "sed -i 's/20171130_oly_pbjelly/20180103_oly_pbjelly/g' /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n")


# In[7]:


get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# WHOOPS! Copy/paste error. Let's try again...

# In[8]:


get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# #### Need to insert special command to tell PB Jelly that this is NOT on a cluster. Will insert into line #4 of ```Protocol.xml``` file using ```sed```
# 
# Hopefully this adjustment will increase the speed of PB Jelly on Emu.

# In[9]:


get_ipython().run_cell_magic('bash', '', "sed -i '4i    <command>${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &</command>' /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n")


# In[10]:


get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[11]:


get_ipython().run_cell_magic('bash', '', 'source /home/shared/PBSuite_15.8.24/setup.sh\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[12]:


get_ipython().run_cell_magic('bash', '', 'source ~/.bashrc\nsource ~/.bash_aliases\nemailme\n')


# #### Fixed spacing of newly inserted line.

# In[13]:


get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[14]:


get_ipython().run_cell_magic('bash', '', 'source /home/shared/PBSuite_15.8.24/setup.sh\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[15]:


get_ipython().run_cell_magic('bash', '', "sed -i 's/\\&/\\&amp;/g' /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n")


# In[16]:


get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[ ]:


get_ipython().run_cell_magic('bash', '', 'source /home/shared/PBSuite_15.8.24/setup.sh\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml\n')


# In[ ]:


get_ipython().run_cell_magic('bash', '', 'source ~/.bashrc\nsource ~/.bash_aliases\nemailme\n')


# In[ ]: