I have run docker run to generate a file
sudo docker run -i --mount type=bind,src=/home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly,target=/home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly 990210oliver/mycc.docker:v1 MyCC.py /home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly/final_contigs_c10K.fa
This is the message I've got after executing.
20181029_0753
4mer
1_rename.py /home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly/final_contigs_c10K.fa 1000
Seqs >= 1000 : 32551
Minimum contig lengh for first stage clustering: 1236
run Prodigal.
/opt/prodigal.linux -i My.fa -a gene.aa -d gene.nuc -f gbk -o output -s potential_genes.txt
run fetchMG.
run UCLUST.
Get Feature.
2_GetFeatures_4mer.py for fisrt stage clustering
2_GetFeatures_4mer.py for second stage clustering
3_GetMatrix.py 1236 for fisrt stage clustering
22896 contigs entering first stage clustering
Clustering...
1_bhsne.py 20
2_ap.py /opt/ap 500 0
Cluster Correction.
to Split and Merge.
1_ClusterCorrection_Split.py 40 2
2_ClusterCorrection_Merge.py 40
Get contig by cluster.
20181029_0811
I now want to get the files generated by MyCC.py to host.
After reading Copying files from Docker container to host, I tried,
sudo docker cp 642ef90103be:/opt /home/mathed/data
But I got an error message
mkdir /home/mathed/data/opt: permission denied
Is there a way to get the files generated to a directory /home/mathed/data?
Thank you.
I assume your dest path does not exist. Docker cp doc stats that in that case :
SRC_PATH specifies a directory
DEST_PATH does not exist
DEST_PATH is created as a directory and the contents of the source directory are copied into this directory
Thus it is trying to create a directory fro DEST_PATH... and docker must have the rights to do so. According to the owner of the DEST_PATH top existing directory, you may have to either