Add CRAN package support for Wave container builds

src/main/groovy/io/seqera/wave/util/ContainerHelper.groovy

@@ -28,6 +28,7 @@ import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.api.SubmitContainerTokenRequest
 import io.seqera.wave.api.SubmitContainerTokenResponse
 import io.seqera.wave.config.CondaOpts
+import io.seqera.wave.config.CranOpts
 import io.seqera.wave.core.ContainerPlatform
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.builder.BuildFormat
@@ -41,6 +42,10 @@ import static io.seqera.wave.util.DockerHelper.condaFileToSingularityFile
 import static io.seqera.wave.util.DockerHelper.condaPackagesToCondaYaml
 import static io.seqera.wave.util.DockerHelper.condaPackagesToDockerFile
 import static io.seqera.wave.util.DockerHelper.condaPackagesToSingularityFile
+import static io.seqera.wave.util.CranHelper.cranPackagesToDockerFile
+import static io.seqera.wave.util.CranHelper.cranPackagesToSingularityFile
+import static io.seqera.wave.util.CranHelper.cranFileToDockerFile
+import static io.seqera.wave.util.CranHelper.cranFileToSingularityFile
 /**
  * Container helper methods
  *
@@ -78,6 +83,23 @@ class ContainerHelper {
             return result
         }
 
+        if( spec.type == PackagesSpec.Type.CRAN ) {
+            if( !spec.cranOpts )
+                spec.cranOpts = new CranOpts()
+            def result
+            if ( spec.entries ) {
+                final String packages = spec.entries.join(' ')
+                result = formatSingularity
+                        ? cranPackagesToSingularityFile(packages, spec.channels, spec.cranOpts)
+                        : cranPackagesToDockerFile(packages, spec.channels, spec.cranOpts)
+            } else {
+                result = formatSingularity
+                        ? cranFileToSingularityFile(spec.cranOpts)
+                        : cranFileToDockerFile(spec.cranOpts)
+            }
+            return result
+        }
+
         throw new BadRequestException("Unexpected packages spec type: $spec.type")
     }
 

src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy

@@ -28,6 +28,7 @@ import io.seqera.wave.api.ImageNameStrategy
 import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.api.SubmitContainerTokenRequest
 import io.seqera.wave.config.CondaOpts
+import io.seqera.wave.config.CranOpts
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.request.ContainerRequest
 import io.seqera.wave.service.builder.BuildFormat
@@ -603,4 +604,73 @@ class ContainerHelperTest extends Specification {
 
     }
 
+    def 'should create cran docker file with packages'() {
+        given:
+        def REPOSITORIES = ['cran', 'bioconductor']
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1', basePackages: 'littler r-cran-docopt'])
+        def PACKAGES = ['dplyr', 'ggplot2', 'bioc::GenomicRanges']
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, entries: PACKAGES, channels: REPOSITORIES, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, false)
+
+        then:
+        result.contains('FROM rocker/r-ver:4.4.1')
+        result.contains('install2.r')
+        result.contains("'dplyr' 'ggplot2' BiocManager::install('GenomicRanges')")
+        result.contains('R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
+    def 'should create cran singularity file with packages'() {
+        given:
+        def REPOSITORIES = ['cran']
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1'])
+        def PACKAGES = ['tidyverse', 'data.table']
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, entries: PACKAGES, channels: REPOSITORIES, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, true)
+
+        then:
+        result.contains('BootStrap: docker')
+        result.contains('From: rocker/r-ver:4.4.1')
+        result.contains('install2.r')
+        result.contains("'tidyverse' 'data.table'")
+        result.contains('export R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
+    def 'should create cran docker file without packages (file mode)'() {
+        given:
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1'])
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, false)
+
+        then:
+        result.contains('FROM rocker/r-ver:4.4.1')
+        result.contains('COPY --from=wave_context_dir . .')
+        result.contains('renv.lock')
+        result.contains('install.R')
+        result.contains('R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
+    def 'should create cran singularity file without packages (file mode)'() {
+        given:
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1', basePackages: 'build-essential'])
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, true)
+
+        then:
+        result.contains('BootStrap: docker')
+        result.contains('From: rocker/r-ver:4.4.1')
+        result.contains('%files')
+        result.contains('/opt/wave_context_dir')
+        result.contains('build-essential')
+        result.contains('renv.lock')
+        result.contains('export R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
 }

typespec/models/ContainerRequest.tsp

@@ -1,5 +1,5 @@
 import "./ContainerConfig.tsp";
-import "./CondaPackages.tsp";
+import "./PackagesSpec.tsp";
 import "./ScanMode.tsp";
 import "./ScanLevel.tsp";
 
@@ -39,8 +39,8 @@ model ContainerRequest {
   @doc("The name strategy to be used to create the name of the container built by Wave. Its values can be `none`, `tagPrefix`, or `imageSuffix`. ")
   nameStrategy?: "none" | "tagPrefix" | "imageSuffix";
   mirror?: boolean;
-  @doc("Conda packages to be installed in the container.")
-  packages?: CondaPackages;
+  @doc("Packages to be installed in the container.")
+  packages?: PackagesSpec;
   scanMode?: ScanMode;
   scanLevels?: ScanLevel[];
   @doc("Request submission timestamp using ISO-8601.")

typespec/models/CranOpts.tsp

@@ -0,0 +1,14 @@
+@doc("Options for CRAN/R environments.")
+@example(#{
+    rImage: "rocker/r-ver:4.4.1",
+    basePackages: "littler r-cran-docopt",
+    commands: #["apt-get update", "apt-get install -y libcurl4-openssl-dev"]
+})
+model CranOpts {
+  @doc("Name of the R Docker image used to build CRAN containers.")
+  rImage: string;
+  @doc("Names of base system packages to install.")
+  basePackages: string;
+  @doc("Commands to be included in the container.")
+  commands: string[];
+}

typespec/models/PackagesSpec.tsp

@@ -0,0 +1,23 @@
+import "./CondaOpts.tsp";
+import "./CranOpts.tsp";
+
+@doc("Specification for packages to be installed in a container.")
+@example(#{
+    type: "CONDA",
+    entries: #["salmon", "bwa"],
+    channels: #["conda-forge", "bioconda"]
+})
+model PackagesSpec {
+  @doc("The type of package manager: CONDA or CRAN.")
+  type: "CONDA" | "CRAN";
+  @doc("The package environment file encoded as a base64 string.")
+  environment?: string;
+  @doc("A list of one or more package names.")
+  entries?: string[];
+  @doc("Conda build options (when type is CONDA).")
+  condaOpts?: CondaOpts;
+  @doc("CRAN build options (when type is CRAN).")
+  cranOpts?: CranOpts;
+  @doc("Channels or repositories used for downloading packages.")
+  channels?: string[];
+}

wave-api/src/main/java/io/seqera/wave/api/PackagesSpec.java

@@ -21,6 +21,7 @@
 import java.util.Objects;
 
 import io.seqera.wave.config.CondaOpts;
+import io.seqera.wave.config.CranOpts;
 
 /**
  * Model a Package environment requirements
@@ -29,7 +30,7 @@
  */
 public class PackagesSpec {
 
-    public enum Type { CONDA }
+    public enum Type { CONDA, CRAN }
 
     public Type type;
 
@@ -48,6 +49,11 @@ public enum Type { CONDA }
      */
     public CondaOpts condaOpts;
 
+    /**
+     * CRAN build options
+     */
+    public CranOpts cranOpts;
+
     /**
      * channels used for downloading packages
      */
@@ -62,12 +68,13 @@ public boolean equals(Object object) {
                 && Objects.equals(environment, that.environment)
                 && Objects.equals(entries, that.entries)
                 && Objects.equals(condaOpts, that.condaOpts)
+                && Objects.equals(cranOpts, that.cranOpts)
                 && Objects.equals(channels, that.channels);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(type, environment, entries, condaOpts, channels);
+        return Objects.hash(type, environment, entries, condaOpts, cranOpts, channels);
     }
 
     @Override
@@ -77,6 +84,7 @@ public String toString() {
                 ", envFile='" + environment + '\'' +
                 ", packages=" + entries +
                 ", condaOpts=" + condaOpts +
+                ", cranOpts=" + cranOpts +
                 ", channels=" + ObjectUtils.toString(channels) +
                 '}';
     }
@@ -106,4 +114,9 @@ public PackagesSpec withCondaOpts(CondaOpts opts) {
         return this;
     }
 
+    public PackagesSpec withCranOpts(CranOpts opts) {
+        this.cranOpts = opts;
+        return this;
+    }
+
 }

wave-api/src/main/java/io/seqera/wave/config/CranOpts.java

@@ -0,0 +1,83 @@
+/*
+ * Copyright 2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package io.seqera.wave.config;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+/**
+ * CRAN/R build options
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+public class CranOpts {
+    final public static String DEFAULT_R_IMAGE = "rocker/r-ver:4.4.1";
+    final public static String DEFAULT_PACKAGES = "littler r-cran-docopt";
+
+    public String rImage;
+    public List<String> commands;
+    public String basePackages;
+
+    public CranOpts() {
+        this(Map.of());
+    }
+
+    public CranOpts(Map<String,?> opts) {
+        this.rImage = opts.containsKey("rImage") ? opts.get("rImage").toString(): DEFAULT_R_IMAGE;
+        this.commands = opts.containsKey("commands") ? (List<String>)opts.get("commands") : null;
+        this.basePackages = opts.containsKey("basePackages") ? (String)opts.get("basePackages") : DEFAULT_PACKAGES;
+    }
+
+    public CranOpts withRImage(String value) {
+        this.rImage = value;
+        return this;
+    }
+
+    public CranOpts withCommands(List<String> value) {
+        this.commands = value;
+        return this;
+    }
+
+    public CranOpts withBasePackages(String value) {
+        this.basePackages = value;
+        return this;
+    }
+
+    @Override
+    public String toString() {
+        return String.format("CranOpts(rImage=%s; basePackages=%s, commands=%s)",
+                rImage,
+                basePackages,
+                commands != null ? String.join(",", commands) : "null"
+                );
+    }
+
+    @Override
+    public boolean equals(Object object) {
+        if (this == object) return true;
+        if (object == null || getClass() != object.getClass()) return false;
+        CranOpts cranOpts = (CranOpts) object;
+        return Objects.equals(rImage, cranOpts.rImage) && Objects.equals(commands, cranOpts.commands) && Objects.equals(basePackages, cranOpts.basePackages);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(rImage, commands, basePackages);
+    }
+}

wave-utils/src/main/java/io/seqera/wave/util/Base32.java

@@ -32,7 +32,7 @@ public final class Base32 {
             -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, // `abcdefghijklmno
             15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 // pqrstuvwxyz
     };
-    /* Messsages for Illegal Parameter Exceptions in decode() */
+    /* Messages for Illegal Parameter Exceptions in decode() */
     private static final String errorCanonicalLength = "non canonical Base32 string length";
     private static final String errorCanonicalEnd = "non canonical bits at end of Base32 string";
     private static final String errorInvalidChar = "invalid character in Base32 string";