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stjude / CICERO

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
https://stjude.github.io/CICERO
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singularity error #43

Closed alhafidzhamdan closed 3 years ago

alhafidzhamdan commented 3 years ago

Hi there, My HPC does not allow direct docker use so i'm using singularity instead to build the docker image. Using this command:

singularity --verbose --debug build cicero.simg docker://stjude/cicero:0.3.0

DEBUG   [U=2341426,P=350718]persistentPreRunE()           Singularity version: 3.5.0+dirty
DEBUG   [U=2341426,P=350718]handleConfDir()               /home/mhamdan/.singularity already exists. Not creating.
DEBUG   [U=2341426,P=350718]getCacheBasedir()             environment variable SINGULARITY_CACHEDIR not set, using default image cache
DEBUG   [U=2341426,P=350718]updateCacheSubdir()           Caching directory set to /home/mhamdan/.singularity/cache/library
DEBUG   [U=2341426,P=350718]updateCacheSubdir()           Caching directory set to /home/mhamdan/.singularity/cache/oci-tmp
DEBUG   [U=2341426,P=350718]updateCacheSubdir()           Caching directory set to /home/mhamdan/.singularity/cache/oci
DEBUG   [U=2341426,P=350718]updateCacheSubdir()           Caching directory set to /home/mhamdan/.singularity/cache/net
DEBUG   [U=2341426,P=350718]updateCacheSubdir()           Caching directory set to /home/mhamdan/.singularity/cache/shub
DEBUG   [U=2341426,P=350718]updateCacheSubdir()           Caching directory set to /home/mhamdan/.singularity/cache/oras
DEBUG   [U=2341426,P=350718]newBundle()                   Created temporary directory "/tmp/bundle-temp-170087539" for the bundle
DEBUG   [U=2341426,P=350718]newBundle()                   Created directory "/tmp/rootfs-e8fe5976-38c8-11eb-ab90-6c2b59b4600d" for the bundle
DEBUG   [U=2341426,P=350718]ensureGzipComp()              Ensuring gzip compression for mksquashfs
DEBUG   [U=2341426,P=350718]ensureGzipComp()              Gzip compression by default ensured
INFO    [U=2341426,P=350718]Full()                        Starting build...
DEBUG   [U=2341426,P=350718]Get()                         Reference: stjude/cicero:0.3.0
DEBUG   [U=2341426,P=350718]cleanUp()                     Cleaning up "/tmp/rootfs-e8fe5976-38c8-11eb-ab90-6c2b59b4600d" and "/tmp/bundle-temp-170087539"
FATAL   [U=2341426,P=350718]runBuildLocal()               While performing build: conveyor failed to get: Error reading manifest 0.3.0 in docker.io/stjude/cicero: errors:
denied: requested access to the resource is denied
unauthorized: authentication required

It says authentication required- i'm not sure if i've done anything wrong with the command? Appreciate any input. A

adthrasher commented 3 years ago

Due to licensing restrictions, we do not provide pre-built Docker images. So there is no stjude/cicero:0.3.0 image on Docker hub from which Singularity can build. You will need to build the Docker image on a machine that allows Docker. You could then build the Singularity image from that and transfer it to your HPC to run.

alhafidzhamdan commented 3 years ago

Perfect- thanks for that, much appreciated