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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
69 stars 17 forks source link

When building docker image ,come on a error #102

Closed yonglpy closed 3 years ago

yonglpy commented 3 years ago

when using Dockerfile to build image,the following message appears: Step 51/81 : COPY build/Rprofile $OPT/config/Rprofile COPY failed: stat /var/lib/docker/tmp/docker-builder005224817/build/Rprofile: no such file or directory Has anyone encountered such a problem when building a mirror?

keiranmraine commented 3 years ago

Can you confirm which tag or commit of the repository was in use? Also are you sure the local file system wasn't full?

FYI you don't need to build the image it can be downloaded from Quay.io by tag: https://quay.io/repository/wtsicgp/ascatngs

e.g.

docker pull quay.io/wtsicgp/ascatngs:4.5.0

or for singularity:

singularity pull docker://quay.io/wtsicgp/ascatngs:4.5.0
sotaro-kanematsu commented 3 years ago

Hi keiranmraine I am going to use ascatNGS to uncover allele-specific somatic copy number alternations in clinical samples (tumor-normal pair). I pull the docker images as you explained as above, however, I don't know how to handle the docker images to get results because I am only a beginner.
Could you teach me the example command using docker images to get the list of allele-specific somatic copy number alternations? In addition to that, I would like to know how to construct SnpGcCorrections.tsv file under the docker enviornment.

keiranmraine commented 3 years ago

@sotaro-kanematsu please see: https://github.com/cancerit/ascatNgs/wiki/Basic-usage#docker