text: user7476: I want to use MEGAHIT (git: https://github.com/voutcn/megahit) to assemble metagenome shotgun sequencing reads (illumina). 
  I install the package with the command conda install -c bioconda megahit as described in on the github page which yields: 
  Solving environment: done
  
  ## Package Plan ##
  
    environment location: /home/datura-workstation/miniconda3
  
    added / updated specs:
      - megahit
  
  
  The following NEW packages will be INSTALLED:
  
    megahit            bioconda/linux-64::megahit-1.2.9-h8b12597_0
  
  
  Proceed ([y]/n)?
  
  Where I click yes and the packages is installed. However, after installation I am not able to use the command megahit as this results in the error: megahit: command not found.
  I use Ubuntu 18.04.3 LTS and have installed miniconda3.
  I reproduced the installation of megahit on a windows computer with a virtual machine using the same Ubuntu version. On my virtual Ubuntu I CAN use the megahit command.
  Could anyone please help me solve this problem? I searched the internet but cannot find a good solution on the issue (also not on the github issue page of this package).
  
  user3381: type conda info --envs.  Look at your list of environments.  Say it's base that has megahit in it, do conda activate base, then just do megahit. 
  
original_text: 7476: <p>I want to use <code>MEGAHIT</code> (git: <a href="https://github.com/voutcn/megahit" rel="nofollow noreferrer">https://github.com/voutcn/megahit</a>) to assemble metagenome shotgun sequencing reads (illumina). </p>
  
  <p>I install the package with the command <code>conda install -c bioconda megahit</code> as described in on the github page which yields: </p>
  
  <pre><code>Solving environment: done
  
  ## Package Plan ##
  
    environment location: /home/datura-workstation/miniconda3
  
    added / updated specs:
      - megahit
  
  
  The following NEW packages will be INSTALLED:
  
    megahit            bioconda/linux-64::megahit-1.2.9-h8b12597_0
  
  
  Proceed ([y]/n)?
  </code></pre>
  
  <p>Where I click yes and the packages is installed. However, after installation I am not able to use the command <code>megahit</code> as this results in the error: <code>megahit: command not found</code>.</p>
  
  <p>I use Ubuntu 18.04.3 LTS and have installed <code>miniconda3</code>.</p>
  
  <p>I reproduced the installation of <code>megahit</code> on a windows computer with a virtual machine using the same Ubuntu version. On my virtual Ubuntu I CAN use the <code>megahit</code> command.</p>
  
  <p>Could anyone please help me solve this problem? I searched the internet but cannot find a good solution on the issue (also not on the github issue page of this package).</p>
   3381: <p>type <code>conda info --envs</code>.  Look at your list of environments.  Say it's <code>base</code> that has <code>megahit</code> in it, do <code>conda activate base</code>, then just do <code>megahit</code>. </p>
  