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perun_and_environments

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perun_and_environments [2018/06/27 15:54] – 129.173.90.41perun_and_environments [2018/12/12 11:06] (current) – 129.173.90.41
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 ====== Using environments on perun ====== ====== Using environments on perun ======
  
 +Below you will find the instructions about how to find and run software **IF it is under CONDA**. You should always check if the software you need is under conda as an **outdated** version of it may be in the environmental variables of the cluster. Since not all software available in perun can be run under an environment there are other places where you could check **[[other_software_locations|]]** and if your software requires databases check **[[databases_locations|]]**.
  
 Perun has conda installed.  Perun has conda installed. 
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-''**conda --version**''+''**conda %%--version%%**'' or ''**conda -V**''
  
 To see the list of all the environments on perun (it is very long!) To see the list of all the environments on perun (it is very long!)
  
-''**conda info --envs**''+''**conda info %%--envs%%**'' 
  
 The output should look like this at the top The output should look like this at the top
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 To search the list you can do something like this To search the list you can do something like this
  
-**''conda info --envs |grep blast''**+''**conda info %%--envs%% |grep blast **''\\ 
 +or\\ 
 +''**conda env list |grep blast ]**''\\
  
 This will provide you with all the environments with the string blast in them\\ This will provide you with all the environments with the string blast in them\\
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 SO, SO,
-to invoke an environment in a qsub shell +to invoke an environment in a qsub shell: 
- +----------------------------------------------------------------- 
-''**export PATH=/scratch2/software/anaconda/bin:$PATH**'' +''**#!/bin/bash**''\\ 
- +''**#$ -S /bin/bash**''\\ 
-''**source activate nameofenvironment**''+''**. /etc/profile**''\\ 
 +''**#$ -cwd**''\\ 
 +''**export PATH=/scratch2/software/anaconda/bin:$PATH**''\\ 
 +''**source activate nameofenvironment**'' [or ''**conda activate nameofenvironment**'']\\ 
 +''**your command line **''\\ 
 +''**source deactivate**''\\ 
 +------------------------------------------------------------------
  
 Some of the more common environments you might be interested in Some of the more common environments you might be interested in
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 ''**source activate python36-generic**'' ''**source activate python36-generic**''
 +
 +**You are already in the environment and do not know what to do next**\\
 +
 +1- invoke the executable command (see your software manual).\\
 +
 +2- if no manual is available and you still don't know what executable to call:\\
 +
 +**let's say you want to use trnascan:**\\
 + conda env list|grep 'trnascan' \\
 + trnascan-se              /scratch2/software/anaconda/envs/trnascan-se\\
 + ls /scratch2/software/anaconda/envs/trnascan-se/bin/\\
 + then select your executable and directly invoke it within the environment:\\
 + tRNAscan-SE
 +
 +
 +
  
  
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