Init test version 2.0.0

CHANGES.md

@@ -8,3 +8,13 @@ Initial Version.
 
 Version 0.0.3 for astrocyte release. Tested on astrocyte live.
 
+2021-08-04
+----------
+
+Version 0.0.9 for testing of astrocyte 1.0.0 is released. In this version singularity was enabled to run the workflow.
+
+2022-08-09
+----------
+Test version 2.0.0 for testing of astrocyte 2.0.0 is released.
+
+This version provide an example on how to pull images from customized registry, e.g. git.biohpc.swmed.edu:5050 (See the `workflow_containers` section in `astrocyte_pkg.yml`), and how to call the image with relative path in the nextflow configure file (See the `process` section of `workflow/configs/biohpc.config`).

README.md

@@ -21,12 +21,17 @@ There is a single parameter `story`. This provides 1 or more files that the
 workflow should run on.
 
 ## Containers
+### Astrocyte workflow containers
+
+The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the contianers used by this workflow. When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to `workflow/images/singularity/` for later use.  
+In the workflow, the default configuration located in `workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes.
+
+### Vizapp containers
+
+The `astrocyte_cli` version 2.0.0 supports containerized vizapp, so that vizapp becomes more independent and can be run on multiple platforms. The astrocyte workflow developers do not need to change their `vizapp_*` settings in `astrocyte_pkg.yml` to use this feature. The `shiny-prepare` command with the `--with-container` option will pull the right version of `R` container from the BioHPC "[Astrocyte Container Images](https://git.biohpc.swmed.edu/biohpc/astrocyte-container-images)" registry and save it to the `vizapp` folder for later use. Also, it will create a folder `vizapp/.rlibrary` to install the dependencies pacages.
 
-The default configuration for this workflow is located in ./workflow/configs/biohpc.config . This configuration will cause the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes, using Docker.io endpoints. The biohpc_*_gitlab.config files show how to instead use images pulled from a specified GitLab repository.
 
 ## Questions
 
 If you have any questions about this workflow example, or Astrocyte in general,
 please contact the BioHPC team via biohpc-help@utsouthwestern.edu
-
-

astrocyte_pkg.yml

@@ -31,11 +31,11 @@ citation: |
   
 # The minimum Astrocyte version that requires to run this workflow. For old pipelines, which do not have this label 
 # a default value of 0.3.1 will be assigned automatically. A request of minimum version less than 0.4.0 will be ignored.
-minimum_astrocyte_version: '0.4.1'
+minimum_astrocyte_version: '2.0.0'
 # The Nextflow version that requires to run this workflow.  For old pipelines, which do not have this label 
 # a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
 # in the module list.
-nextflow_version: '21.04.1'
+nextflow_version: '22.04.5'
 # (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
 nextflow_config: 'biohpc.config'
 # The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
@@ -66,12 +66,16 @@ documentation_files:
 # Specify versioned module names to ensure reproducability.
 workflow_modules:
   - Test
+
 # A list of container images requires to run this workflow.
 # Specify full path and version names to ensure reproducability.
-# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above
+# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above.
+# Singularity supports different registries, please specify the protocol to use.
+# Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
+# container registry of BioHPC to save and manage your container images.
 workflow_containers:
-  - docker://ubuntu:latest
-  - docker://centos:centos8
+  - docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest
+  - docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:
@@ -171,7 +175,8 @@ workflow_parameters:
 #            The workflow must publish all final output into $baseDir
 
 # Name of the R module that the vizapp will run against
-vizapp_r_module: 'R/3.6.1-gccmkl'
+# A containerized version is recommanded.
+vizapp_r_module: 'R/4.1.1-img'
 
 # List of any CRAN packages, not provided by the modules, that must be made
 # available to the vizapp

workflow/configs/biohpc.config

 singularity {
   enabled = true
-  runOptions = '--disable-cache'                                // use this one for production
-  // runOptions = '--disable-cache --bind /vagrant:/vagrant'    // use this one for vagrant development env only
-  cacheDir = "$baseDir/images/singularity"
+  runOptions = ''                             // Please do NOT use "--disable-cache" in this runOptions. 
+                                              // Starting from version 2.0.0, the astrocyte_cli will clean up the cache automatically.
+  // runOptions = '--bind /vagrant:/vagrant'  // Use this one for vagrant development env only
+  cacheDir = "$baseDir/images/singularity"    // Singularity images specified in `workflow_containers` of astrocyte_pkg.yml will be saved to 
+                                              // this folder automatically, before running the workflow. The images will be renamed as
+                                              // "NAME-TAG.img", e.g. ubuntu-latest.img, centos-centos8.img, r-4.1.1.img, etc.
 }
 
 process {
     executor = 'local'
     withName:parameters {
-        container = 'docker://ubuntu:latest'
+        // Path to the singularity image files. The prefix "file://images/singularity/" is the cacheDir folder 
+        // in the singularity settings. Please keep this prefix for the path of your singularity images
+        container = 'file://images/singularity/ubuntu-latest.img'
     }
     withName:uppercase {
-        container = 'docker://ubuntu:latest'
+        container = 'file://images/singularity/ubuntu-latest.img'
     }
     withName:tolines {
-        container = 'docker://ubuntu:latest'
+        container = 'file://images/singularity/ubuntu-latest.img'
     }
     withName:wordcounts {
-        container = 'docker://centos:centos8'
+        container = 'file://images/singularity/centos-centos8.img'
     }
 }

workflow/configs/biohpc_docker.config

-docker {
-  enabled = true
-  fixOwnership = true
-}
-
-
-process {
-    executor = 'local'
-    withName:uppercase {
-        container = 'ubuntu:latest'
-    }
-    withName:tolines {
-        container = 'ubuntu:latest'
-    }
-    withName:wordcounts {
-        container = 'centos:centos8'
-    }
-}

workflow/configs/biohpc_docker_gitlab.config

-docker {
-  enabled = true
-  fixOwnership = true
-}
-
-
-process {
-    executor = 'local'
-    withName:uppercase {
-        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
-    }
-    withName:tolines {
-        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
-    }
-    withName:wordcounts {
-        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8'
-    }
-}

workflow/configs/biohpc_singularity_gitlab.config

-singularity {
-  enabled = true
-  runOptions = '--disable-cache'                                // use this one for production
-  // runOptions = '--disable-cache --bind /vagrant:/vagrant'    // use this one for vagrant development env only
-  cacheDir = "$baseDir/images/singularity"
-}
-
-
-process {
-    executor = 'local'
-    withName:parameters {
-        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
-    }
-    withName:uppercase {
-        container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
-    }
-    withName:tolines {
-        container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
-    }
-    withName:wordcounts {
-        container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8'
-    }
-}

workflow/main.nf

 /*
- * Copyright (c) 2016. The University of Texas Southwestern Medical Center
+ * Copyright (c) 2022. The University of Texas Southwestern Medical Center
  *
  *   This file is part of the BioHPC Workflow Platform
  *
  * This is a minimal test workflow package that astrocyte tests can run against.
  *
  * @authors
- * David Trudgian, Peng Lian, Devin OKelly
+ * Peng Lian
  *
  */
 
@@ -41,6 +41,8 @@ process parameters {
     echo "test_string: ${params.test_string}"
     echo "test_select: ${params.test_select}"
     echo "test_multiselect: ${params.test_multiselect}"
+
+    sleep 1
     """
 }