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Default networking for docker run changed?

See original GitHub issue

Hello. Today I updated cwltool on my machine from cwltool-1.0.20190228155703 to latest cwltool-1.0.20190618201008. After this update all my pipelines became broken. As I discovered from starter log - default options for docker run changed. cwltool-1.0.20190228155703:

$ cwltool --outdir /home/bio/test vep.cwl_schema.yml vep.val_test.yml
[job vep.cwl_schema.yml] /tmp/uk7ve30p$ docker \                                                                            
    run \                                                                                                                   
    -i \                                                                                                                    
    --volume=/tmp/uk7ve30p:/JlOrjE:rw \                                                                                     
    --volume=/tmp/omihujk3:/tmp:rw \                                                                                        
    --volume=/home/bio/REPOs/varscan.all.all.hc.fp-filtered-D3.Somatic.vcf:/var/lib/cwl/stga0d0fe86-05d0-4a3f-a971-8b41d1192227/varscan.all.all.hc.fp-filtered-D3.Somatic.vcf:ro \
    --workdir=/JlOrjE \                                                                                                     
    --read-only=true \                                                                                                      
    --user=1000:1000 \                                                                                                      
    --rm \                                                                                                                  
    --env=TMPDIR=/tmp \                                                                                                     
    --env=HOME=/JlOrjE \                                                                                                    
    --cidfile=/tmp/_lle2che/20190620182526-906933.cid \                                                                     
    nexus.cspmz.ru:8443/vep:v0.3.13 \                                                                                       
    --sample-name \                                                                                                         
    E07002 \                                                                                                                
    --genome-build \                                                                                                        
    GRCh38.d1.vd1 \                                                                                                         
    --opts-for-neo \                                                                                                        
    true \                                                                                                                  
    --opts-for-maf \                                                                                                        
    true \                                                                                                                  
    --extra-opts \                                                                                                          
    '' \                                                                                                                    
    --output-dir \                                                                                                          
    out_workdir \                                                                                                           
    --output-gz \                                                                                                           
    E07002.vep_logs.tar.gz \                                                                                                
    --output-vcf \                                                                                                          
    E07002.annot-vep.vcf \                                                                                                  
    /var/lib/cwl/stga0d0fe86-05d0-4a3f-a971-8b41d1192227/varscan.all.all.hc.fp-filtered-D3.Somatic.vcf

cwltool-1.0.20190618201008:

$ cwltool --outdir /home/bio/test vep.cwl_schema.yml vep.val_test.yml
[job vep] /tmp/5gf7pbvv$ docker \                                                                                           
    run \                                                                                                                   
    -i \                                                                                                                    
    --volume=/tmp/5gf7pbvv:/CJnsMo:rw \                                                                                     
    --volume=/tmp/ir3qpfrr:/tmp:rw \                                                                                        
    --volume=/home/bio/REPOs/varscan.all.all.hc.fp-filtered-D3.Somatic.vcf:/var/lib/cwl/stg7665d317-d0e4-4fed-ad18-d1caa7c96c11/varscan.all.all.hc.fp-filtered-D3.Somatic.vcf:ro \                                                                      
    --workdir=/CJnsMo \                                                                                                     
    --read-only=true \                                                                                                      
    --net=none \                                                                                                            
    --user=1000:1000 \                                                                                                      
    --rm \                                                                                                                  
    --env=TMPDIR=/tmp \                                                                                                     
    --env=HOME=/CJnsMo \                                                                                                    
    --cidfile=/tmp/s5iqmorx/20190620183825-019022.cid \                                                                     
    nexus.cspmz.ru:8443/vep:v0.3.13 \                                                                                       
    --sample-name \                                                                                                         
    E07002 \                                                                                                                
    --genome-build \                                                                                                        
    GRCh38.d1.vd1 \                                                                                                         
    --opts-for-neo \                                                                                                        
    true \                                                                                                                  
    --opts-for-maf \                                                                                                        
    true \                                                                                                                  
    --extra-opts \                                                                                                          
    '' \                                                                                                                    
    --output-dir \                                                                                                          
    out_workdir \                                                                                                           
    --output-gz \                                                                                                           
    E07002.vep_logs.tar.gz \                                                                                                
    --output-vcf \                                                                                                          
    E07002.annot-vep.vcf \                                                                                                  
    /var/lib/cwl/stg7665d317-d0e4-4fed-ad18-d1caa7c96c11/varscan.all.all.hc.fp-filtered-D3.Somatic.vcf

As you can see - network switched to ‘none’. Is this intended? And if yes - can you help me to fix my settings to reproduce old behaviour?

Issue Analytics

State:
Created 4 years ago
Reactions:2
Comments:14 (9 by maintainers)

Top GitHub Comments

2reactions

tetroncommented, Jun 20, 2019

Thanks, I can reproduce the bug now, I will keep looking at it.

1reaction

tetroncommented, Jun 20, 2019

Thanks. Unfortunately I still don’t have an explanation.

What happens if you run this?

cwlVersion: v1.0
class: CommandLineTool
requirements:
  DockerRequirement:
    dockerPull: tutum/curl
inputs: []
outputs: []
arguments: [curl, -L, http://commonwl.org]

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