cromwell refuses to connect to internal registry

genome · Aug 10, 2022 · 78b377e · 78b377e
1 parent 2018f97
commit 78b377e
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/definitions/tools/aligned_seq_fda_stats.cwl b/definitions/tools/aligned_seq_fda_stats.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 baseCommand: ['/usr/bin/perl', 'aligned_stats.pl']
 requirements:
     - class: DockerRequirement
-      dockerPull: "registry.gsc.wustl.edu/apipe-builder/genome_perl_environment:compute1-52"
+      dockerPull: "mgibio/cle:v1.4.2"
     - class: ResourceRequirement
       ramMin: 16000
     - class: StepInputExpressionRequirement
@@ -86,7 +86,7 @@ requirements:
 
                 # specifies the program paths
                 # docker(registry.gsc.wustl.edu/apipe-builder/genome_perl_environment:compute1-52)
-                $samtools = "/usr/bin/samtools";                                  # Version: 1.10 (using htslib 1.10.2-3)
+                $samtools = "/opt/samtools/bin/samtools";                                  # Version: 1.10 (using htslib 1.10.2-3)
 
 
 

diff --git a/definitions/tools/unaligned_seq_fda_stats.cwl b/definitions/tools/unaligned_seq_fda_stats.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 baseCommand: ['/usr/bin/perl', 'unaligned_stats.pl']
 requirements:
     - class: DockerRequirement
-      dockerPull: "registry.gsc.wustl.edu/apipe-builder/genome_perl_environment:compute1-52"
+      dockerPull: "mgibio/cle:v1.4.2"
     - class: ResourceRequirement
       ramMin: 16000
     - class: StepInputExpressionRequirement
@@ -92,7 +92,7 @@ requirements:
                 # docker(registry.gsc.wustl.edu/apipe-builder/genome_perl_environment:compute1-52)
                 $bzcat = "/usr/bin/bzcat";                                             # Version 1.0.8
                 $zcat = "/usr/bin/zcat";                                                # zcat (gzip) 1.10
-                $samtools = "/usr/bin/samtools";                                  # Version: 1.10 (using htslib 1.10.2-3)
+                $samtools = "/opt/samtools/bin/samtools";                                  # Version: 1.10 (using htslib 1.10.2-3)
 
                 # specifies the N letter to count
                 # (default: "N")