Add support for Spack packages to Singularity build

Signed-off-by: Paolo Di Tommaso <[email protected]>
seqeralabs · Sep 6, 2023 · dfb5fc3 · dfb5fc3
1 parent 5f3168b
commit dfb5fc3
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Showing 4 changed files with 35 additions and 5 deletions.
diff --git a/app/build.gradle b/app/build.gradle
@@ -21,7 +21,7 @@ repositories {
 
 dependencies {
     implementation 'io.seqera:wave-api:0.5.0'
-    implementation 'io.seqera:wave-utils:0.7.2'
+    implementation 'io.seqera:wave-utils:0.7.3'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.squareup.moshi:moshi:1.14.0'
     implementation 'com.squareup.moshi:moshi-adapters:1.14.0'

diff --git a/app/conf/resource-config.json b/app/conf/resource-config.json
@@ -20,6 +20,8 @@
     "pattern":"\\Qtemplates/conda/singularityfile-conda-packages.txt\\E"
   }, {
     "pattern":"\\Qtemplates/spack/dockerfile-spack-file.txt\\E"
+  }, {
+    "pattern":"\\Qtemplates/spack/singularityfile-spack-file.txt\\E"
   }, {
     "pattern":"java.base:\\Qjdk/internal/icu/impl/data/icudt72b/nfc.nrm\\E"
   }, {

diff --git a/app/src/main/java/io/seqera/wavelit/App.java b/app/src/main/java/io/seqera/wavelit/App.java
@@ -39,7 +39,6 @@
 import io.seqera.wave.api.SubmitContainerTokenResponse;
 import io.seqera.wave.config.CondaOpts;
 import io.seqera.wave.config.SpackOpts;
-import io.seqera.wave.util.DockerHelper;
 import io.seqera.wave.util.DockerIgnoreFilter;
 import io.seqera.wave.util.Packer;
 import io.seqera.wavelit.exception.BadClientResponseException;
@@ -57,6 +56,8 @@
 import static io.seqera.wave.util.DockerHelper.condaFileToSingularityFile;
 import static io.seqera.wave.util.DockerHelper.condaPackagesToDockerFile;
 import static io.seqera.wave.util.DockerHelper.condaPackagesToSingularityFile;
+import static io.seqera.wave.util.DockerHelper.spackFileToDockerFile;
+import static io.seqera.wave.util.DockerHelper.spackFileToSingularityFile;
 import static io.seqera.wave.util.DockerHelper.spackPackagesToSpackFile;
 import static io.seqera.wavelit.util.Checkers.isEmpty;
 import static io.seqera.wavelit.util.Checkers.isEnvVar;
@@ -530,7 +531,9 @@ protected String containerFileBase64() {
 
         if( !isEmpty(spackFile) || spackPackages!=null ) {
             final SpackOpts opts = new SpackOpts() .withCommands(spackRunCommands);
-            final String result = DockerHelper.spackFileToDockerFile(opts);
+            final String result = singularity
+                        ? spackFileToSingularityFile(opts)
+                        : spackFileToDockerFile(opts);
             return encodeStringBase64(result);
         }
 

diff --git a/app/src/test/groovy/io/seqera/wavelit/AppSpackOptsTest.groovy b/app/src/test/groovy/io/seqera/wavelit/AppSpackOptsTest.groovy
@@ -128,7 +128,10 @@ class AppSpackOptsTest extends Specification {
         and:
         def req = app.createRequest()
         then:
-        new String(req.containerFile.decodeBase64()).startsWith("# Runner image")
+        def spec = new String(req.containerFile.decodeBase64()).tokenize('\n')
+        spec[0] == '# Runner image'
+        spec[1] == 'FROM {{spack_runner_image}}'
+        spec[2] == 'COPY --from=builder /opt/spack-env /opt/spack-env'
 
         and:
         new String(req.spackFile.decodeBase64()) == '''\
@@ -146,7 +149,6 @@ class AppSpackOptsTest extends Specification {
                 "--spack-package", "bar",
                 "--spack-run-command", "RUN one",
                 "--spack-run-command", "RUN two",
-
         ]
 
         when:
@@ -166,4 +168,27 @@ class AppSpackOptsTest extends Specification {
                 '''.stripIndent(true)
     }
 
+    def 'should create container file from spack package with singularity' () {
+        given:
+        def app = new App()
+        String[] args = ["--spack-package", "foo", "--singularity"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        and:
+        def req = app.createRequest()
+        then:
+        def spec = new String(req.containerFile.decodeBase64()).tokenize('\n')
+        spec[0] == 'Bootstrap: docker'
+        spec[1] == 'From: {{spack_runner_image}}'
+        spec[2] == 'stage: final'
+
+        and:
+        new String(req.spackFile.decodeBase64()) == '''\
+                spack:
+                  specs: [foo]
+                  concretizer: {unify: true, reuse: false}
+                '''.stripIndent(true)
+    }
+
 }