Answers.Body: <p>Bit of an old post sorry, but I think you might be getting a little confused here. The nf-core pipelines come with their own software already, so you don't need to install or bootstrap optitype yourself. If it's used in the pipeline, it comes in the pipeline container(s) (or conda environment or whatever packaging system you use). So you should never have to touch <code>docker://fred2/optitype</code>.</p>
  <p>When you run the pipeline with the <code>-profile singularity</code> argument, it will automatically pull the image from Docker Hub and convert to Singularity for you <em>(some of the newer pipelines pull pre-build Singularity images directly)</em>. You can also use the <code>nf-core download hlatyping --singularity</code> command from the helper tools to pull the image ahead of time.</p>
  <ul>
  <li>Docker images for this pipeline: <a href="https://hub.docker.com/r/nfcore/hlatyping" rel="nofollow noreferrer">https://hub.docker.com/r/nfcore/hlatyping</a></li>
  <li>Documentation for this pipeline: <a href="https://nf-co.re/hlatyping/" rel="nofollow noreferrer">https://nf-co.re/hlatyping/</a></li>
  <li>nf-core/tools download docs: <a href="https://nf-co.re/tools/#downloading-pipelines-for-offline-use" rel="nofollow noreferrer">https://nf-co.re/tools/#downloading-pipelines-for-offline-use</a></li>
  </ul>
  <p>I hope this helps! Come and <a href="https://nf-co.re/join" rel="nofollow noreferrer">join the nf-core Slack organisation</a> if you need more help. We have a channel for each pipeline, including <code>#hlatyping</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-19T22:08:00.103Z
Answers.LastActivityDate: 2021-04-19T22:08:00.103Z
Answers.UserDisplayName: ewels
Body: <p>I am trying to use <code>optitype</code> on an HPC without docker support or sudo privileges. A search brought me <a href="https://github.com/researchapps/optitype" rel="nofollow noreferrer">https://github.com/researchapps/optitype</a> and <a href="https://github.com/nf-core/hlatyping" rel="nofollow noreferrer">https://github.com/nf-core/hlatyping</a>. I tried bootstrapping the singularity image as follows:</p>
  <pre><code>singularity build optitype.simg docker://fred2/optitype
  </code></pre>
  <p>However, this does not seem to run as expected. Could someone with experience bootstrapping docker files onto singularity suggest how I could change this? How do the commands change when doing a bootstrap? I would appreciate your help!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-09T09:02:39.113Z
Comments.Text: 'Not as expected' is a little vague. Alternatively try to build from https://hub.docker.com/r/nfcore/hlatyping
Comments.UserDisplayName: Pallie
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-09T20:26:31.423Z
Comments.Text: Have you just tried the singularity container? https://biocontainers.pro/#/tools/optitype
Comments.UserDisplayName: Devon Ryan
Tags: <docker>
Title: Optitype for Singularity
ThreadText: # Optitype for Singularity
  
  (Asked by: username_0 on 2020-09-09)
  
  I am trying to use `optitype` on an HPC without docker support or sudo privileges. A search brought me <https://github.com/researchapps/optitype> and <https://github.com/nf-core/hlatyping>. I tried bootstrapping the singularity image as follows:
  
  ```
  singularity build optitype.simg docker://fred2/optitype
  
  ```
  
  However, this does not seem to run as expected. Could someone with experience bootstrapping docker files onto singularity suggest how I could change this? How do the commands change when doing a bootstrap? I would appreciate your help!
  
  **Tags:** docker
  
  > **Comments:**
  > **username_1**: 'Not as expected' is a little vague. Alternatively try to build from https://hub.docker.com/r/nfcore/hlatyping  
  > **username_2**: Have you just tried the singularity container? https://biocontainers.pro/#/tools/optitype  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2021-04-19. Score: 1
  
  Bit of an old post sorry, but I think you might be getting a little confused here. The nf-core pipelines come with their own software already, so you don't need to install or bootstrap optitype yourself. If it's used in the pipeline, it comes in the pipeline container(s) (or conda environment or whatever packaging system you use). So you should never have to touch `docker://fred2/optitype`.
  
  When you run the pipeline with the `-profile singularity` argument, it will automatically pull the image from Docker Hub and convert to Singularity for you *(some of the newer pipelines pull pre-build Singularity images directly)*. You can also use the `nf-core download hlatyping --singularity` command from the helper tools to pull the image ahead of time.
  
  * Docker images for this pipeline: <https://hub.docker.com/r/nfcore/hlatyping>
  * Documentation for this pipeline: <https://nf-co.re/hlatyping/>
  * nf-core/tools download docs: <https://nf-co.re/tools/#downloading-pipelines-for-offline-use>
  
  I hope this helps! Come and [join the nf-core Slack organisation](https://nf-co.re/join) if you need more help. We have a channel for each pipeline, including `#hlatyping`.
  
  
  ---
  
  