/opt incorrect for udocker in udocker
Created by: amcpherson
I am running udocker within udocker but the /opt of the inner image is not correct, and is instead that of the outer image.
Example:
/opt/conda/bin/hmmcopy_single_cell.R
is present in the singlecellpipeline/hmmcopy:v0.0.5
image:
$ udocker run --nosysdirs --user $USER -w $PWD -v $PWD:$PWD --rm -e ROOT_HOME=/home/mcphersa1 docker.io/singlecellpipeline/hmmcopy:v0.0.5 /bin/bash -i
Error: delete not owner: /home/azureuser/.udocker/containers/ebecf120-0d81-31da-ab5e-1d67472cd707/ROOT/etc/alternatives/pager.1.gz
Error: this container exposes privileged TCP/IP ports
Warning: non-existing user will be created
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* *
* STARTING ebecf120-0d81-31da-ab5e-1d67472cd707 *
* *
******************************************************************************
executing: bash
$ ls -lah /opt/conda/bin/hmmcopy_single_cell.R
-rwxrwxr-x 2 azureuser G1000 16K Apr 16 12:51 /opt/conda/bin/hmmcopy_single_cell.R
If i run the singlecellpipeline/single_cell_pipeline:v0.5.6
image then use udocker to run singlecellpipeline/hmmcopy:v0.0.5
within that then /opt/conda/bin/hmmcopy_single_cell.R
is not present. The contents of /opt/conda/bin
matches that of the outer image singlecellpipeline/single_cell_pipeline:v0.5.6
$ udocker run --user $USER -w $PWD -v $PWD:$PWD -v $HOME:$HOME -v /data:/data --rm docker.io/singlecellpipeline/single_cell_pipeline:v0.5.6 /bin/bash -i
Error: delete not owner: /home/azureuser/.udocker/containers/9b0a42b3-fa43-39f3-86ed-89fb0d329cc0/ROOT/etc/alternatives/pager.1.gz
Error: this container exposes privileged TCP/IP ports
Warning: non-existing user will be created
******************************************************************************
* *
* STARTING 9b0a42b3-fa43-39f3-86ed-89fb0d329cc0 *
* *
******************************************************************************
executing: bash
$ udocker run --nosysdirs --user $USER -w $PWD -v $PWD:$PWD --rm -e ROOT_HOME=/home/mcphersa1 docker.io/singlecellpipeline/hmmcopy:v0.0.5 /bin/bash -i
Info: setup repo: //.udocker
Info: udocker command line interface 1.1.4
Info: searching for udockertools 1.1.4
Info: installing udockertools 1.1.4
Info: installation of udockertools successful
Downloading layer: sha256:1ab2bdfe97783562315f98f94c0769b1897a05f7b0395ca1520ebee08666703b
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:dd7d28bd8be53eeb346a7895aa923cc5fd8707cd893b5a96f6de37d0473431f8
Downloading layer: sha256:af998e3a361bf15f05a9cf4686abe0bc34affbb1bb1d541f76553c5842e6e4fb
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:82300909c1f86cd7fb5d91febb53b4b3603fd183f1f3363b1f201c86e454596d
Downloading layer: sha256:75ff01eb431f296cb0cd1bc8512d6c22048b917714f838cbced4396cd80bd6aa
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:f19f63f3d37038c31d8a3a063e5093dc936e5e910afb8669da591b4c4cc68ebf
Downloading layer: sha256:cf914e3a87c4f0da1d832e88baa8850c2bd50df6aeb8af5b6a1bbb193d1087c1
Downloading layer: sha256:1b1dd755f7624be7648f2bcadd89f379af322e2058411dd20d95c8153999db1d
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Error: this container exposes privileged TCP/IP ports
Warning: non-existing user will be created
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* *
* STARTING b883ee8a-e415-3acb-a51a-fc90b6def18e *
* *
******************************************************************************
executing: bash
$ ls /opt/conda/bin/hmmcopy_single_cell.R
ls: cannot access '/opt/conda/bin/hmmcopy_single_cell.R': No such file or directory