Answers.Body: <p>@terdon answered that</p>
  <pre><code>docker run -v /data/Continuum/WES/:/gatk/vcf -it broadinstitute/gatk:latest
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-10T21:07:20.083Z
Answers.Text: Glad it's solved. Unless @terdon posts this as an answer, could you kindly mark this as "resolved" please (this helps with site stats). The "resolved" flag can always be shifted between posts, i.e. if terdon answers later.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-11T09:14:22.490Z
Answers.Text: I do not know how to do that sorry
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-12T12:13:40.940Z
Answers.Text: Just "accept" your answer (see https://bioinformatics.stackexchange.com/help/someone-answers) by clicking on the checkmark on the left.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-10T19:00:00.933Z
Answers.LastActivityDate: 2023-08-10T19:00:00.933Z
Answers.UserDisplayName: Zizogolu
Body: <p>I have pulled GATK docker on my computer but when running a GATK command, can not locate my input file</p>
  <p><strong>My OS version</strong></p>
  <pre><code>cat /etc/os-release
  NAME=&quot;Ubuntu&quot;
  VERSION=&quot;18.04.6 LTS (Bionic Beaver)&quot;
  ID=ubuntu
  ID_LIKE=debian
  PRETTY_NAME=&quot;Ubuntu 18.04.6 LTS&quot;
  VERSION_ID=&quot;18.04&quot;
  HOME_URL=&quot;https://www.ubuntu.com/&quot;
  SUPPORT_URL=&quot;https://help.ubuntu.com/&quot;
  BUG_REPORT_URL=&quot;https://bugs.launchpad.net/ubuntu/&quot;
  PRIVACY_POLICY_URL=&quot;https://www.ubuntu.com/legal/terms-and-policies/privacy-policy&quot;
  VERSION_CODENAME=bionic
  UBUNTU_CODENAME=bionic
  </code></pre>
  <p>Files in my working directory</p>
  <pre><code>fi1d18@RBGO-Server2:/data/Continuum/WES/vcf<span class="math-container">$ ls
  GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
  NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup.bam
  NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup.bam.bai
  NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDuplicates.txt
  NG-27280_CLTSS_LTS_001B_lib506242_7915_2_MarkedDup.bam
  NG-27280_CLTSS_LTS_001B_lib506242_7915_2_MarkedDup.bam.bai
  NG-27280_CLTSS_LTS_001B_lib506242_7915_2_MarkedDuplicates.txt
  NG-27280_CLTSS_LTS_002B_lib488377_7494_1_MarkedDup.bam
  NG-27280_CLTSS_LTS_002B_lib488377_7494_1_MarkedDup.bam.bai
  NG-27280_CLTSS_LTS_002B_lib488377_7494_1_MarkedDuplicates.txt
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$</span> 
  </code></pre>
  <p>I then pulled GATK docker</p>
  <pre><code>fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ docker run -v ~/vcf:/gatk/vcf -it broadinstitute/gatk:latest
  (gatk) root@8b2af4d7aadf:/gatk# 
  
  
  (gatk) root@8b2af4d7aadf:/gatk# ls
  GATKConfig.EXAMPLE.properties  gatk-package-4.4.0.0-local.jar  gatkPythonPackageArchive.zip  scripts
  README.md              gatk-package-4.4.0.0-spark.jar  gatkcondaenv.yml          vcf
  gatk                   gatk-spark.jar              gatkenv.rc
  gatk-completion.sh         gatk.jar                run_unit_tests.sh
  (gatk) root@8b2af4d7aadf:/gatk# 
  </code></pre>
  <p>As you see, folder seems to be empty because I can not connect my local working directory to container</p>
  <pre><code>(gatk) root@6d3d3ff69e21:/gatk# cd vcf
  (gatk) root@6d3d3ff69e21:/gatk/vcf# ls
  (gatk) root@6d3d3ff69e21:/gatk/vcf# 
  </code></pre>
  <p>I have tried all of these but did not work</p>
  <pre><code>fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ docker run -v /data/Continuum/WES/vc:/gatk/ -it broadinstitute/gatk:latest
  
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ docker run -v ~/data/Continuum/WES/vc:/gatk/ -it broadinstitute/gatk:latest
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-10T17:20:00.287Z
Comments.Text: What does `-v ~/vcf:/gatk/vcf` do? Why are you using `~/vcf` there? `~` is your `$HOME` directory, is `/data/Continuum/WES/` your home directory? Does it work if you try `docker run -v /data/Continuum/WES/:/gatk/vcf  -it broadinstitute/gatk:late`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-10T17:59:13.943Z
Comments.Text: Yes you solved that, thanks a lot
Comments.UserDisplayName: Zizogolu
Tags: <gatk><docker><wes>
Title: Importing local files to a GATK docker image
ThreadText: # Importing local files to a GATK docker image
  
  (Asked by: username_0 on 2023-08-10)
  
  I have pulled GATK docker on my computer but when running a GATK command, can not locate my input file
  
  **My OS version**
  
  ```
  cat /etc/os-release
  NAME="Ubuntu"
  VERSION="18.04.6 LTS (Bionic Beaver)"
  ID=ubuntu
  ID_LIKE=debian
  PRETTY_NAME="Ubuntu 18.04.6 LTS"
  VERSION_ID="18.04"
  HOME_URL="https://www.ubuntu.com/"
  SUPPORT_URL="https://help.ubuntu.com/"
  BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
  PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
  VERSION_CODENAME=bionic
  UBUNTU_CODENAME=bionic
  
  ```
  
  Files in my working directory
  
  ```
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ ls
  GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
  NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup.bam
  NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup.bam.bai
  NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDuplicates.txt
  NG-27280_CLTSS_LTS_001B_lib506242_7915_2_MarkedDup.bam
  NG-27280_CLTSS_LTS_001B_lib506242_7915_2_MarkedDup.bam.bai
  NG-27280_CLTSS_LTS_001B_lib506242_7915_2_MarkedDuplicates.txt
  NG-27280_CLTSS_LTS_002B_lib488377_7494_1_MarkedDup.bam
  NG-27280_CLTSS_LTS_002B_lib488377_7494_1_MarkedDup.bam.bai
  NG-27280_CLTSS_LTS_002B_lib488377_7494_1_MarkedDuplicates.txt
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ 
  
  ```
  
  I then pulled GATK docker
  
  ```
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ docker run -v ~/vcf:/gatk/vcf -it broadinstitute/gatk:latest
  (gatk) root@8b2af4d7aadf:/gatk# 
  
  (gatk) root@8b2af4d7aadf:/gatk# ls
  GATKConfig.EXAMPLE.properties  gatk-package-4.4.0.0-local.jar  gatkPythonPackageArchive.zip  scripts
  README.md              gatk-package-4.4.0.0-spark.jar  gatkcondaenv.yml          vcf
  gatk                   gatk-spark.jar              gatkenv.rc
  gatk-completion.sh         gatk.jar                run_unit_tests.sh
  (gatk) root@8b2af4d7aadf:/gatk# 
  
  ```
  
  As you see, folder seems to be empty because I can not connect my local working directory to container
  
  ```
  (gatk) root@6d3d3ff69e21:/gatk# cd vcf
  (gatk) root@6d3d3ff69e21:/gatk/vcf# ls
  (gatk) root@6d3d3ff69e21:/gatk/vcf# 
  
  ```
  
  I have tried all of these but did not work
  
  ```
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ docker run -v /data/Continuum/WES/vc:/gatk/ -it broadinstitute/gatk:latest
  
  fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ docker run -v ~/data/Continuum/WES/vc:/gatk/ -it broadinstitute/gatk:latest
  
  ```
  
  **Tags:** gatk, docker, wes
  
  > **Comments:**
  > **username_1**: What does `-v ~/vcf:/gatk/vcf` do? Why are you using `~/vcf` there? `~` is your `$HOME` directory, is `/data/Continuum/WES/` your home directory? Does it work if you try `docker run -v /data/Continuum/WES/:/gatk/vcf  -it broadinstitute/gatk:late`?  
  > **username_0**: Yes you solved that, thanks a lot  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2023-08-10. Score: 1 | Accepted answer
  
  @username_1 answered that
  
  ```
  docker run -v /data/Continuum/WES/:/gatk/vcf -it broadinstitute/gatk:latest
  
  ```
  
  > **Comments:**
  > **username_2**: Glad it's solved. Unless @username_1 posts this as an answer, could you kindly mark this as "resolved" please (this helps with site stats). The "resolved" flag can always be shifted between posts, i.e. if username_1 answers later.  
  > **username_0**: I do not know how to do that sorry  
  > **username_1**: Just "accept" your answer (see https://bioinformatics.stackexchange.com/help/someone-answers) by clicking on the checkmark on the left.  
  
  ---
  
  