Hello,
I am using docker container for my RNAseq analysis. I am also using Windows PowerShell. However, I am quite new in using docker, container, and bash.
At the beginning of RNAseq analysis, I need to perform quality control of my raw data using FastQC. For this, I am using the container from the workshop. However, first I need to mount my data into the docker container.
I put my raw data folder into my pen drive (USB flash drive), and the path of my data folder is F:\mary. Mary folder contains 10 fastq.gz data files with different names (e.g. 20120215_WT_5_R1.fastq.gz).
I would highly appreciate if you can help me that how can I mount my data into the container.
How can I find that what is the data directory in container in my pc? Should I create a folder somewhere in my pc? or there is already a place in the container that I should just find its path? What should I write in the below code in the question mark part?
$ docker run -d -p port in host:port in container -v F:\mary: ????? name of the container
Many thanks for your help.
Best wishes,
1 answer
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Don't exactly know the difference in PC. There are generally two ways. Assuming the contents of the folder you're adding do not change post-build, you can define something like
ADD . /directory/inside/the/containerin yourDockerfileand rundockeras usual. Alternatively, you can usedocker run -v /directory/of/your/computer:/directory/inside/the/container ....To use docker run -v /directory/of/your/computer:/directory/inside/the/container ....
May I know what is "the directory inside the container" that I should use? and also how can I find this directory?