Use BioContainers Docker images by default.

bigdatagenomics · Jan 9, 2018 · 9859e3e · 9859e3e
1 parent 5e9db0a
commit 9859e3e
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala
@@ -47,8 +47,8 @@ class BowtieArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
   @Args4jOption(required = false, name = "-bowtie_path", usage = "Path to the Bowtie executable. Defaults to bowtie.")
   var bowtiePath: String = "bowtie"
 
-  @Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/bowtie.")
-  var dockerImage: String = "heuermh/bowtie"
+  @Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bowtie.")
+  var dockerImage: String = "quay.io/biocontainers/bowtie"
 
   @Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch Bowtie. If false, uses the Bowtie executable path.")
   var useDocker: Boolean = false

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala
@@ -47,8 +47,8 @@ class Bowtie2Args extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
   @Args4jOption(required = false, name = "-bowtie2_path", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
   var bowtie2Path: String = "bowtie2"
 
-  @Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to heuermh/bowtie2.")
-  var dockerImage: String = "heuermh/bowtie2"
+  @Args4jOption(required = false, name = "-docker_image", usage = "Docker image to use. Defaults to quay.io/biocontainers/bowtie2.")
+  var dockerImage: String = "quay.io/biocontainers/bowtie2"
 
   @Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch Bowtie 2. If false, uses the Bowtie 2 executable path.")
   var useDocker: Boolean = false