Body: <p>I'm trying to run <a href="https://genome-blog.soe.ucsc.edu/blog/2017/03/17/how-portable-is-your-track-hub-use-hubcheck-to-find-out/" rel="nofollow noreferrer">hubCheck utility</a>* from inside Kubernetes Pod but for some reason I get this Network error:</p>
  <pre><code># I ran hubCheck hubCheck from inside the pod
  $ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
  ### kent source version 431 ###
  Found 2 problems:
  Couldn't open ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
  TCP non-blocking connect() to ftp.ebi.ac.uk IP 193.62.193.138 timed-out in select() after 10000 milliseconds - Cancelling!
  </code></pre>
  <p>However, when I run <code>hubCheck</code> locally it works fine.</p>
  <pre><code>$ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
  ### kent source version 430 ###
  1 tracks in sacCer3
  1 tracks in mm10
  1 tracks in ce10
  1 tracks in galGal4
  1 tracks in ci2
  1 tracks in danRer7
  1 tracks in dm6
  1 tracks in hg38
  </code></pre>
  <p>The first thing I checked is if the pod has access to the internet, which was the case as you can see below, I can use curl to download <code>hubCheck</code>:</p>
  <pre><code># curl -o tools/hubCheck http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hubCheck
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  100 33.2M  100 33.2M    0     0  10.0M      0  0:00:03  0:00:03 --:--:-- 10.0M
  </code></pre>
  <p>I thought this may be caused by a firewall limiting the access to external URL, but I don't think it's the case because other URLs like the one below is working fine both outside and inside K8s:</p>
  <pre><code>$ ./hubCheck -noTracks -verbose=2 http://younglab.wi.mit.edu/mESC_ChIAPET_hub/hub.txt
  ### kent source version 431 ###
  4 tracks in mm9
  </code></pre>
  <p>Any help on this would be greatly appreciated!</p>
  <hr />
  <ul>
  <li>hub Check is a database which facilitates online UCSC Genome Browser display</li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-14T12:38:56.883Z
Comments.Text: There are not many Kubernetes users here, but you never know. This question is perhaps better answered via UCSC's online support
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-14T13:16:01.623Z
Comments.Text: @M__, Thank you, I think I'll do that, I asked on SO but the question didn't get enough attention
Comments.UserDisplayName: Bilal
Tags: <networks><ucsc>
Title: Running hubCheck utility from inside K8s's Pod
ThreadText: # Running hubCheck utility from inside K8s's Pod
  
  (Asked by: username_0 on 2022-06-14)
  
  I'm trying to run [hubCheck utility](https://genome-blog.soe.ucsc.edu/blog/2017/03/17/how-portable-is-your-track-hub-use-hubcheck-to-find-out/)\* from inside Kubernetes Pod but for some reason I get this Network error:
  
  ```
  # I ran hubCheck hubCheck from inside the pod
  $ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
  ### kent source version 431 ###
  Found 2 problems:
  Couldn't open ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
  TCP non-blocking connect() to ftp.ebi.ac.uk IP 193.62.193.138 timed-out in select() after 10000 milliseconds - Cancelling!
  
  ```
  
  However, when I run `hubCheck` locally it works fine.
  
  ```
  $ ./hubCheck -noTracks -verbose=2 ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt
  ### kent source version 430 ###
  1 tracks in sacCer3
  1 tracks in mm10
  1 tracks in ce10
  1 tracks in galGal4
  1 tracks in ci2
  1 tracks in danRer7
  1 tracks in dm6
  1 tracks in hg38
  
  ```
  
  The first thing I checked is if the pod has access to the internet, which was the case as you can see below, I can use curl to download `hubCheck`:
  
  ```
  # curl -o tools/hubCheck http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hubCheck
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  100 33.2M  100 33.2M    0     0  10.0M      0  0:00:03  0:00:03 --:--:-- 10.0M
  
  ```
  
  I thought this may be caused by a firewall limiting the access to external URL, but I don't think it's the case because other URLs like the one below is working fine both outside and inside K8s:
  
  ```
  $ ./hubCheck -noTracks -verbose=2 http://younglab.wi.mit.edu/mESC_ChIAPET_hub/hub.txt
  ### kent source version 431 ###
  4 tracks in mm9
  
  ```
  
  Any help on this would be greatly appreciated!
  
  ---
  
  * hub Check is a database which facilitates online UCSC Genome Browser display
  
  **Tags:** networks, ucsc
  
  > **Comments:**
  > **username_1**: There are not many Kubernetes users here, but you never know. This question is perhaps better answered via UCSC's online support  
  > **username_0**: @username_1, Thank you, I think I'll do that, I asked on SO but the question didn't get enough attention  
  
  ---
  
  ## 0 answers
  
  