diff --git a/README.md b/README.md index 39b0e4b..5ada515 100644 --- a/README.md +++ b/README.md @@ -117,7 +117,6 @@ docker run $container sh -c 'bamtools --version && samtools --version' cat << EOF > ./conda.yaml name: my-conda channels: - - defaults - bioconda - conda-forge dependencies: diff --git a/app/src/main/java/io/seqera/wave/cli/App.java b/app/src/main/java/io/seqera/wave/cli/App.java index e338bfa..eaef4f4 100644 --- a/app/src/main/java/io/seqera/wave/cli/App.java +++ b/app/src/main/java/io/seqera/wave/cli/App.java @@ -158,7 +158,7 @@ public class App implements Runnable { private List condaRunCommands; @Option(names = {"--conda-channels"}, paramLabel = "''", description = "Conda channels used to build the container (default: ${DEFAULT-VALUE}).") - private String condaChannels = "seqera,conda-forge,bioconda,defaults"; + private String condaChannels = "conda-forge,bioconda"; @Option(names = {"--spack-file"}, paramLabel = "''", description = "A Spack file used to build the container e.g. /some/path/spack.yaml.") private String spackFile; diff --git a/app/src/main/java/io/seqera/wave/cli/util/GptHelper.java b/app/src/main/java/io/seqera/wave/cli/util/GptHelper.java index 860b628..b28e464 100644 --- a/app/src/main/java/io/seqera/wave/cli/util/GptHelper.java +++ b/app/src/main/java/io/seqera/wave/cli/util/GptHelper.java @@ -117,7 +117,7 @@ static protected PackagesSpec jsonToPackageSpec(String json) { throw new IllegalArgumentException("Unable to resolve packages from json response: " + json); List channels = (List) object.get("channels"); if( Checkers.isEmpty(channels) ) - channels = List.of("bioconda","conda-forge","defaults"); + channels = List.of("bioconda","conda-forge"); return new PackagesSpec() .withType(PackagesSpec.Type.CONDA) .withEntries(packages) diff --git a/app/src/test/groovy/io/seqera/wave/cli/AppCondaOptsTest.groovy b/app/src/test/groovy/io/seqera/wave/cli/AppCondaOptsTest.groovy index 51b5e78..e8b9276 100644 --- a/app/src/test/groovy/io/seqera/wave/cli/AppCondaOptsTest.groovy +++ b/app/src/test/groovy/io/seqera/wave/cli/AppCondaOptsTest.groovy @@ -141,7 +141,7 @@ class AppCondaOptsTest extends Specification { '''.stripIndent(true) and: req.packages.condaOpts == new CondaOpts(mambaImage: CondaOpts.DEFAULT_MAMBA_IMAGE, basePackages: CondaOpts.DEFAULT_PACKAGES) - req.packages.channels == ['seqera', 'conda-forge', 'bioconda', 'defaults'] + req.packages.channels == ['conda-forge', 'bioconda'] and: !req.packages.entries and: @@ -166,7 +166,7 @@ class AppCondaOptsTest extends Specification { req.packages.entries == ['foo'] and: req.packages.condaOpts == new CondaOpts(mambaImage: CondaOpts.DEFAULT_MAMBA_IMAGE, basePackages: CondaOpts.DEFAULT_PACKAGES) - req.packages.channels == ['seqera', 'conda-forge', 'bioconda', 'defaults'] + req.packages.channels == ['conda-forge', 'bioconda'] and: !req.packages.environment and: @@ -187,7 +187,7 @@ class AppCondaOptsTest extends Specification { req.packages.entries == ['https://host.com/file-lock.yml'] and: req.packages.condaOpts == new CondaOpts(mambaImage: CondaOpts.DEFAULT_MAMBA_IMAGE, basePackages: CondaOpts.DEFAULT_PACKAGES) - req.packages.channels == ['seqera', 'conda-forge', 'bioconda', 'defaults'] + req.packages.channels == ['conda-forge', 'bioconda'] and: !req.packages.environment and: diff --git a/app/src/test/groovy/io/seqera/wave/cli/util/GptHelperTest.groovy b/app/src/test/groovy/io/seqera/wave/cli/util/GptHelperTest.groovy index 8f03686..847924f 100644 --- a/app/src/test/groovy/io/seqera/wave/cli/util/GptHelperTest.groovy +++ b/app/src/test/groovy/io/seqera/wave/cli/util/GptHelperTest.groovy @@ -45,6 +45,6 @@ class GptHelperTest extends Specification { when: def spec = GptHelper.grabPackages("Give me a container image for multiqc 1.15") then: - spec == new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: ['multiqc=1.15'], channels: ['bioconda','conda-forge','defaults']) + spec == new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: ['multiqc=1.15'], channels: ['bioconda','conda-forge']) } }