<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>

CC BY-SA 4.0
2019-02-26T22:21:49.853Z
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.
Devon Ryan
CC BY-SA 4.0
2019-02-27T11:05:38.857Z
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.
Biomagician
CC BY-SA 4.0
2019-02-25T15:13:30.647Z
2019-02-25T15:13:30.647Z
Biomagician
<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>

CC BY-SA 4.0
2019-02-25T14:52:18.670Z
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?
Daniel Standage
<software-installation><snakemake><bioconda><anaconda>
Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?
# 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.  

---

