conda-incubator/conda-env-builder

Found a cyclical dependency in the environment inheritance misreported

nh13 opened this issue · 0 comments

nh13 commented

I would expect that the error would be "inherited environment samtools does not exist". Instead we get "Found a cyclical dependency in the environment inheritance."

Input YAML

name: example
environments:
  defaults:
    steps:
      - conda:
          channels:
            - conda-forge
            - bioconda
          requirements:
            - bwa=0.7.17
            - python=3.6.10
  bwa:
    group: alignment
    inherits:
      - samtools
    steps:
      - conda:
          requirements:
            - samtools
            - bwa
conda-env-builder Compile -c config.yaml 
...
[2020/12/15 21:31:19 | CondaEnvironmentBuilderMain | Info] Executing Compile from conda-env-builder version 010c473 as nhomer@nils-fg.local on JRE 1.8.0_192-b01
[2020/12/15 21:31:19 | CondaEnvironmentBuilderMain | Info] Compile failed. Elapsed time: 0.02 minutes.
Exception in thread "main" java.lang.IllegalArgumentException: Found a cyclical dependency in the environment inheritance.
	at com.github.nh13.condaenvbuilder.api.Spec$.com$github$nh13$condaenvbuilder$api$Spec$$compile(Spec.scala:160)
	at com.github.nh13.condaenvbuilder.api.Spec.compiled(Spec.scala:22)
	at com.github.nh13.condaenvbuilder.tools.Compile.execute(Compile.scala:30)
	at com.github.nh13.condaenvbuilder.cmdline.CondaEnvironmentBuilderMain.makeItSo(CondaEnvironmentBuilderMain.scala:62)
	at com.github.nh13.condaenvbuilder.cmdline.CondaEnvironmentBuilderMain.makeItSoAndExit(CondaEnvironmentBuilderMain.scala:47)
	at com.github.nh13.condaenvbuilder.cmdline.CondaEnvironmentBuilderMain$.main(CondaEnvironmentBuilderMain.scala:20)
	at com.github.nh13.condaenvbuilder.cmdline.CondaEnvironmentBuilderMain.main(CondaEnvironmentBuilderMain.scala)