Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-28T08:16:13.013Z
Answers.Text: even in the ```base``` environment, the command ```megahit``` is not found.
Answers.UserDisplayName: RobH
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-28T08:39:28.780Z
Answers.Text: I re-installed ```megahit``` and now when I activate ```conda activate base```, ```megahit``` does work. Thank you!!
Answers.UserDisplayName: RobH
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-28T06:41:31.707Z
Answers.LastActivityDate: 2020-04-28T06:41:31.707Z
Answers.UserDisplayName: user3479780
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-27T13:26:16.683Z
Comments.Text: Why not just install Anaconda3?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-27T16:32:58.347Z
Comments.Text: /home/datura-workstation/miniconda3/bin/megahit ? it should be there
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-28T05:35:57.423Z
Comments.Text: Did you run `make install` after building?
Comments.UserDisplayName: Jose Fernando Lopez Fernandez
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-28T07:41:28.440Z
Comments.Text: @ATpoint Ah, gotcha. Thanks
Comments.UserDisplayName: Jose Fernando Lopez Fernandez
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-28T08:23:21.463Z
Comments.Text: In ```minconda3/bin``` there is no executable file named ```megahit```. (I checked the folder on my test virtual machine and there the file is indeed there.) That seems to be the problem. I can find the ```megahit``` on my workstation in the directory ```/home/datura-workstation/miniconda3/pkgs/megahit-1.2.9-h8b12597_0/bin```. Why is it there? Can I just copy these files to the ```miniconda/bin```?  All files of ```megahit``` are placed in this directory while they should be located in the ```miniconda3/bin``` directory.
Comments.UserDisplayName: RobH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-28T08:31:51.420Z
Comments.Text: EDIT: I re-installed ```megahit``` and now there the ```megahit``` files are present in the ```miniconda3/bin```. However, I still receive the error.
Comments.UserDisplayName: RobH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-28T08:38:44.827Z
Comments.Text: EDIT2: after activating ```conda activate base```, ```megahit``` became functional. Thanks all for the help!
Comments.UserDisplayName: RobH
Tags: <assembly>
Title: "megahit: command not found" after correct installation with miniconda
ThreadText: # "megahit: command not found" after correct installation with miniconda
  
  (Asked by: username_0 on 2020-04-27)
  
  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).
  
  **Tags:** assembly
  
  > **Comments:**
  > **username_1**: Why not just install Anaconda3?  
  > **username_2**: /home/datura-workstation/miniconda3/bin/megahit ? it should be there  
  > **username_3**: Did you run `make install` after building?  
  > **username_3**: @ATpoint Ah, gotcha. Thanks  
  > **username_0**: In ```minconda3/bin``` there is no executable file named ```megahit```. (I checked the folder on my test virtual machine and there the file is indeed there.) That seems to be the problem. I can find the ```megahit``` on my workstation in the directory ```/home/datura-workstation/miniconda3/pkgs/megahit-1.2.9-h8b12597_0/bin```. Why is it there? Can I just copy these files to the ```miniconda/bin```?  All files of ```megahit``` are placed in this directory while they should be located in the ```miniconda3/bin``` directory.  
  > **username_0**: EDIT: I re-installed ```megahit``` and now there the ```megahit``` files are present in the ```miniconda3/bin```. However, I still receive the error.  
  > **username_0**: EDIT2: after activating ```conda activate base```, ```megahit``` became functional. Thanks all for the help!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2020-04-28. Score: 2 | Accepted answer
  
  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`.
  
  > **Comments:**
  > **username_0**: even in the ```base``` environment, the command ```megahit``` is not found.  
  > **username_0**: I re-installed ```megahit``` and now when I activate ```conda activate base```, ```megahit``` does work. Thank you!!  
  
  ---
  
  