<p>@terdon answered that</p>
<pre><code>docker run -v /data/Continuum/WES/:/gatk/vcf -it broadinstitute/gatk:latest
</code></pre>

CC BY-SA 4.0
2023-08-10T21:07:20.083Z
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.
M__
CC BY-SA 4.0
2023-08-11T09:14:22.490Z
I do not know how to do that sorry
Zizogolu
CC BY-SA 4.0
2023-08-12T12:13:40.940Z
Just "accept" your answer (see https://bioinformatics.stackexchange.com/help/someone-answers) by clicking on the checkmark on the left.
terdon
CC BY-SA 4.0
2023-08-10T19:00:00.933Z
2023-08-10T19:00:00.933Z
Zizogolu
<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>

CC BY-SA 4.0
2023-08-10T17:20:00.287Z
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`?
terdon
CC BY-SA 4.0
2023-08-10T17:59:13.943Z
Yes you solved that, thanks a lot
Zizogolu
<gatk><docker><wes>
Importing local files to a GATK docker image
# 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

@terdon answered that
docker run -v /data/Continuum/WES/:/gatk/vcf -it broadinstitute/gatk:latest

> **Comments:**
> **username_2**: 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.  
> **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.  

---

