Answers.Body: <p>From your previous questions, it is apparent that your HPC has an odd singularity setup. You could ask you sysadmin about how to navigate it.</p>
  <h2>EDIT</h2>
  <p>After working with OP on chat (and based on previous experience with them), it looks like their sysadmin has <code>mount hostfs</code> enabled in the <code>singularity.conf</code> file, which messes with every container every time. I guess it's easier than letting people bind their directories of choice but anyway, the way to circumvent that is to use <code>--no-mount hostfs</code></p>
  <p>@Indira, always run <code>singularity [exec|shell|run] --no-mount hostfs</code> instead of plain <code>singularity [exec|shell|run]</code>. All containers will then run well and if they error out, it's probably because either the container internally encountered an error or it was unable to access an external resource. What you're running into now is a mix that obscures the real problems and creates a no-win scenario for you.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-06-05T15:25:15.183Z
Answers.LastActivityDate: 2023-06-09T13:41:50.980Z
Answers.LastEditDate: 2023-06-09T13:41:50.980Z
Answers.UserDisplayName: Ram RS
Body: <p>I am trying to using <a href="https://illumina.github.io/NirvanaDocumentation/introduction/getting-started" rel="nofollow noreferrer">Illumina's Nirvana</a> however I can't seem to get it to work despite having the right Singularity path.</p>
  <ol>
  <li>I pulled Nirvana down using</li>
  </ol>
  <pre class="lang-bash prettyprint-override"><code>singularity pull docker://annotation/nirvana:3.14
  </code></pre>
  <ol start="2">
  <li>I found the path to the .dll using the following command:</li>
  </ol>
  <pre class="lang-bash prettyprint-override"><code>singularity exec nirvana_3.14.sif /bin/bash -c &quot;cd /opt/nirvana/ &amp;&amp; ls&quot;
  </code></pre>
  <ol start="3">
  <li>Tried to run the downloader using:</li>
  </ol>
  <pre class="lang-bash prettyprint-override"><code>## Define path to singularity image:
  sif_container=&quot;/path/to/nirvana_3.14.sif&quot;
  
  ## Path in the singularity file:
  sif_path=&quot;/opt/nirvana/Downloader.dll&quot;
  
  ## Data to be placed in
  Data=&quot;path/to/Nirvana/GRCh38/&quot;
  
  #_____________________________________________________________________________________________________________________________________
  
  singularity exec &quot;<span class="math-container">$sif_container" dotnet "$</span>sif_path&quot; --ga GRCh38 --out &quot;$Data&quot;
  
  </code></pre>
  <p>yet it keeps saying <code>ERROR: The top-level output directory directory was not specified. Please use the --out parameter.</code>. I have checked the paths and they are correct and I have specified the data path yet it does not seem to recognize it? I have even moved around the container and the path variables to no avail?</p>
  
Tags: <illumina><singularity>
Title: Singularity and Illumina's Nirvana
ThreadText: # Singularity and Illumina's Nirvana
  
  (Asked by: username_0 on 2023-06-04)
  
  I am trying to using [Illumina's Nirvana](https://illumina.github.io/NirvanaDocumentation/introduction/getting-started) however I can't seem to get it to work despite having the right Singularity path.
  
  1. I pulled Nirvana down using
  
  ```bash
  singularity pull docker://annotation/nirvana:3.14
  
  ```
  
  2. I found the path to the .dll using the following command:
  
  ```bash
  singularity exec nirvana_3.14.sif /bin/bash -c "cd /opt/nirvana/ && ls"
  
  ```
  
  3. Tried to run the downloader using:
  
  ```bash
  ## Define path to singularity image:
  sif_container="/path/to/nirvana_3.14.sif"
  
  ## Path in the singularity file:
  sif_path="/opt/nirvana/Downloader.dll"
  
  ## Data to be placed in
  Data="path/to/Nirvana/GRCh38/"
  
  #_____________________________________________________________________________________________________________________________________
  
  singularity exec "$sif_container" dotnet "$sif_path" --ga GRCh38 --out "$Data"
  
  ```
  
  yet it keeps saying `ERROR: The top-level output directory directory was not specified. Please use the --out parameter.`. I have checked the paths and they are correct and I have specified the data path yet it does not seem to recognize it? I have even moved around the container and the path variables to no avail?
  
  **Tags:** illumina, singularity
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-06-05. Score: 3 | Accepted answer
  
  From your previous questions, it is apparent that your HPC has an odd singularity setup. You could ask you sysadmin about how to navigate it.
  
  ## EDIT
  
  After working with OP on chat (and based on previous experience with them), it looks like their sysadmin has `mount hostfs` enabled in the `singularity.conf` file, which messes with every container every time. I guess it's easier than letting people bind their directories of choice but anyway, the way to circumvent that is to use `--no-mount hostfs`
  
  @username_0, always run `singularity [exec|shell|run] --no-mount hostfs` instead of plain `singularity [exec|shell|run]`. All containers will then run well and if they error out, it's probably because either the container internally encountered an error or it was unable to access an external resource. What you're running into now is a mix that obscures the real problems and creates a no-win scenario for you.
  
  
  ---
  
  