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wiki:2018bioinformatics_software_summit [2018/09/10 15:51]
david [Python modules]
wiki:2018bioinformatics_software_summit [2018/09/10 15:58] (current)
david
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 ====== Downloading,​ installing, and running Bioinformatics software on Summit ====== ====== Downloading,​ installing, and running Bioinformatics software on Summit ======
 +
 +
 +:!: Info only. NOT on the test.
  
 Software on your home computer or laptop tends to come pre-compiled as binaries. Some bioinformatics programs have this option, but others must be installed at the source code level and compiled for your computer. Software on your home computer or laptop tends to come pre-compiled as binaries. Some bioinformatics programs have this option, but others must be installed at the source code level and compiled for your computer.
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 $ module load python/​3.5.1 $ module load python/​3.5.1
 </​code>​ </​code>​
-==== From source ==== 
  
-The python equivalent to ./configure and make is +==== Installing From source ==== 
 + 
 +First: You must use the ''​module''​ command to load the correct version. 
 + 
 +You would download the source, untar it, and cd to the directory. Then, the python equivalent to ./configure and make is 
 <code bash> <code bash>
 $ python setup.py --prefix=$HOME $ python setup.py --prefix=$HOME
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 You may get an error message about the destination not being in your PYTHONPATH. Treat the PYTHONPATH like your PATH variable. Set it inside your ~/​.bash_profile and add the directory that setup.py is expecting You may get an error message about the destination not being in your PYTHONPATH. Treat the PYTHONPATH like your PATH variable. Set it inside your ~/​.bash_profile and add the directory that setup.py is expecting
  
-==== From pip === +==== Installing ​From pip === 
-The program ''​pip''​ is a python package installer/​manager. You must load a python ​+ 
 +As above: You must use the ''​module''​ command to load the correct version. 
 + 
 +The program ''​pip''​ is a python package installer/​manager. You should be able to use pip without making any directories or uncompressing any source. It should do all of this for you, out of the way. 
 + 
 +<code bash> 
 +$ pip install package --prefix=$HOME 
 +</​code>​
  
wiki/2018bioinformatics_software_summit.txt · Last modified: 2018/09/10 15:58 by david