Thanks for that rimelek, so no need to have a username set up in the debian container.
I used the following command
computername:~/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16$ docker run --volume $HOME:$HOME --workdir ${PWD} -u $(id -u):$(id -g) -it nano_tools_debian
which returned
I have no name!@77cfee7fe3d7:/home/name/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16$ ls
AIG357_pass_barcode11_d46709a9_0.fastq docker_nanoplot_output sequencing_summary_AIG357_d46709a9.txt
So I know that the pwd that I’m in on my host has mounted correctly into the debian container, and that the container can see the files that need to be analysed. But it will not run the NanoPlot command in the Dockerfile.
I then used
~$ sudo docker rmi nano_tools_debian
to remove the container and start again with
computername:~/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16$ sudo docker build -t nano_tools_debian .
to build the container again.
The container build finished without any errors.
computername:~/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16$ sudo docker image history nano_tools_debian
IMAGE CREATED CREATED BY SIZE COMMENT
54534dcdaf09 25 minutes ago /bin/sh -c cd minimap2 && make 5.5MB
481941094c15 25 minutes ago /bin/sh -c git clone https://github.com/lh3/… 2.76MB
e9d8f016d99d 27 minutes ago /bin/sh -c pip install pycoQC 82.4MB
d43d0b163cc2 33 minutes ago /bin/sh -c apt-get -y install git 44.9MB
96c1f4cab101 34 minutes ago /bin/sh -c apt-get -y install curl 3.65MB
fbcfa2fb50e5 34 minutes ago /bin/sh -c pip install NanoPlot --upgrade 56.3kB
4ec7e4709ddf 34 minutes ago /bin/sh -c pip install NanoPlot 810MB
901fedd9c902 48 minutes ago /bin/sh -c pip install nanofilt 160MB
acd0f3339d95 49 minutes ago /bin/sh -c apt-get -y install python3-pip 378MB
42da5db31614 55 minutes ago /bin/sh -c apt update && apt upgrade 17.7MB
0c1c1ca57df3 56 minutes ago /bin/sh -c #(nop) MAINTAINER <naqsdarwin> 0B
827e5611389a 7 days ago /bin/sh -c #(nop) CMD ["bash"] 0B
<missing> 7 days ago /bin/sh -c #(nop) ADD file:5259fc086e8295ddb… 124MB
I then removed the comment from Run NanoPlot in the dockerfile (below) and used
computername:~/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16$ docker run --volume $HOME:$HOME --workdir ${PWD} -u $(id -u):$(id -g) -it nano_tools_debian
but with the same result as above.
I have no name!@77cfee7fe3d7:/home/name/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16$ ls
AIG357_pass_barcode11_d46709a9_0.fastq docker_nanoplot_output sequencing_summary_AIG357_d46709a9.txt
I’m not sure why the files are in the container but the container wont run the NanoPlot command.
Any help would be greatly appreciated.
I’m will also edit the name of this thread if you think the name is not suitable.
FROM debian
MAINTAINER <naqsdarwin>
RUN apt update && apt upgrade
RUN apt-get -y install python3-pip
RUN pip install nanofilt
RUN pip install NanoPlot
RUN pip install NanoPlot --upgrade
RUN apt-get -y install curl
RUN apt-get -y install git
RUN git clone https://github.com/lh3/minimap2
RUN cd minimap2 && make
RUN pip install pycoQC
#https://tleonardi.github.io/pycoQC/installation/
#----------------------------------------------------------------------
# The above completes the building of the container
# The below is now using the programs to anaylse data
#----------------------------------------------------------------------
# Nanoplot
RUN NanoPlot --threads 16 --tsv_stats --summary ~/nextflow/pipelines/docker_training/docker_training_b11_slp338_r116/sequencing_summary.txt ---plots hex dot --N50 --title SLP338 --outdir ~/nextflow/pipelines/docker_training/docker_training_b11_slp338_r16/docker_nanoplot_output/
#----------------------------------------------------------------------
# NanoFilt
#RUN cd ~/nextflow/pipelines/docker_training/docker_training_B11_SLP338_R16
#RUN gzip -c AIG*.fastq > docker_training.gz
#RUN gunzip -c docker_training.gz | NanoFilt --headcrop 30 --tailcrop 30
#----------------------------------------------------------------------