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)