Answers.Body: <p>I created a file .condarc in my home directory with the following content:</p>
  
  <pre><code>channels:
    - conda-forge
    - bioconda
    - defaults
  </code></pre>
  
  <p>and it works now. I don't understand why this is necessary though. I thought the channels in the .condarc file would be used if I did not specify them in my command.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-26T22:21:49.853Z
Answers.Text: This seems to be a bug in the version of `conda` you're using, it works in 4.6.4. Note, however, that you needed to add `-c conda-forge` to your original command anyway, since many of the snakemake dependencies come from there.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-27T11:05:38.857Z
Answers.Text: good point about the dependencies. I didn't know about that. I just always give the channel of the package I want to install but it sounds like I also need to give the channel of dependencies. So I'll keep using `-c conda-forge -c bioconda -c r` in all my `conda install` commands.
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-25T15:13:30.647Z
Answers.LastActivityDate: 2019-02-25T15:13:30.647Z
Answers.UserDisplayName: Biomagician
Body: <p>I searched for the package 'snakemake' on my SLURM cluster using:</p>
  
  <p><code>conda search --channel bioconda snakemake</code></p>
  
  <p>and I get many versions, up to 5.4.2.</p>
  
  <p>I then try to install it using:</p>
  
  <p><code>conda install --channel bioconda --yes snakemake=5.4.2</code></p>
  
  <p>but it fails with the following message:</p>
  
  <pre><code>PackagesNotFoundError: The following packages are not available from current channels:
  
    - snakemake
  
  Current channels:
  
    - https://repo.anaconda.com/pkgs/main/linux-64
    - https://repo.anaconda.com/pkgs/main/noarch
    - https://repo.anaconda.com/pkgs/free/linux-64
    - https://repo.anaconda.com/pkgs/free/noarch
    - https://repo.anaconda.com/pkgs/r/linux-64
    - https://repo.anaconda.com/pkgs/r/noarch
    - https://repo.anaconda.com/pkgs/pro/linux-64
    - https://repo.anaconda.com/pkgs/pro/noarch
  </code></pre>
  
  <p>Why?</p>
  
  <p>Why is the bioconda channel not included in the current channels? I thought that was what the <code>--channel bioconda</code> did in my install command.</p>
  
  <p>Note that <code>conda install --channel bioconda --yes samtools=1.9</code> worked fine and installed samtools successfully.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-25T14:52:18.670Z
Comments.Text: I've heard some folks warn that conda is sensitive to the order in which channels are set/configured. I'm not exactly sure what the details are, but maybe that gives you somewhere to start troubleshooting?
Comments.UserDisplayName: Daniel Standage
Tags: <software-installation><snakemake><bioconda><anaconda>
Title: Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?
ThreadText: # Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?
  
  (Asked by: username_0 on 2019-02-25)
  
  I searched for the package 'snakemake' on my SLURM cluster using:
  
  `conda search --channel bioconda snakemake`
  
  and I get many versions, up to 5.4.2.
  
  I then try to install it using:
  
  `conda install --channel bioconda --yes snakemake=5.4.2`
  
  but it fails with the following message:
  
  ```
  PackagesNotFoundError: The following packages are not available from current channels:
  
    - snakemake
  
  Current channels:
  
    - https://repo.anaconda.com/pkgs/main/linux-64
    - https://repo.anaconda.com/pkgs/main/noarch
    - https://repo.anaconda.com/pkgs/free/linux-64
    - https://repo.anaconda.com/pkgs/free/noarch
    - https://repo.anaconda.com/pkgs/r/linux-64
    - https://repo.anaconda.com/pkgs/r/noarch
    - https://repo.anaconda.com/pkgs/pro/linux-64
    - https://repo.anaconda.com/pkgs/pro/noarch
  
  ```
  
  Why?
  
  Why is the bioconda channel not included in the current channels? I thought that was what the `--channel bioconda` did in my install command.
  
  Note that `conda install --channel bioconda --yes samtools=1.9` worked fine and installed samtools successfully.
  
  **Tags:** software-installation, snakemake, bioconda, anaconda
  
  > **Comments:**
  > **username_1**: I've heard some folks warn that conda is sensitive to the order in which channels are set/configured. I'm not exactly sure what the details are, but maybe that gives you somewhere to start troubleshooting?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2019-02-25. Score: 2
  
  I created a file .condarc in my home directory with the following content:
  
  ```
  channels:
    - conda-forge
    - bioconda
    - defaults
  
  ```
  
  and it works now. I don't understand why this is necessary though. I thought the channels in the .condarc file would be used if I did not specify them in my command.
  
  > **Comments:**
  > **username_2**: This seems to be a bug in the version of `conda` you're using, it works in 4.6.4. Note, however, that you needed to add `-c conda-forge` to your original command anyway, since many of the snakemake dependencies come from there.  
  > **username_0**: good point about the dependencies. I didn't know about that. I just always give the channel of the package I want to install but it sounds like I also need to give the channel of dependencies. So I'll keep using `-c conda-forge -c bioconda -c r` in all my `conda install` commands.  
  
  ---
  
  