Merge branch 'develop' into feature/java_21

.circleci/config.yml

@@ -52,7 +52,7 @@ common_jobs: &common_jobs
         - integration-tests:
             matrix:
               parameters:
-                testing_profile: [ "singularity-tests", "bitbucket-tests" ]
+                testing_profile: [ "singularity-tests", "bitbucket-tests", "toil-integration-tests" ]
             <<: *common_filters
             <<: *slack_context
             requires:
@@ -198,7 +198,8 @@ jobs:
             - run:
                 name: findDevelopSnapshot
                 command: |
-                  ./mvnw versions:update-properties -Dincludes=io.dockstore:* -DallowSnapshots
+                  # grab the latest snapshot version that doesn't seem to correspond to a feature branch or similar
+                  ./mvnw versions:update-properties -Dincludes="io.dockstore:*" -Dmaven.version.ignore=\.*-\.*-SNAPSHOT -DallowSnapshots
             - run:
                 name: force update to latest snapshot versions, # review this step to see what versions were used, also see https://stackoverflow.com/questions/29020716/maven-what-does-u-update-snapshots-really-do
                 command: |

.github/workflows/deploy_artifacts.yml

@@ -0,0 +1,16 @@
+name: Deploy artifacts
+
+on:
+  push:
+    tags: 
+      - '**'
+    branches-ignore:
+      - 'master'
+      - 'release/**'
+      - 'hotfix/**'
+      - 'dependabot/**'
+
+jobs:
+  build:
+    uses: dockstore/workflow-actions/.github/workflows/deploy_artifacts.yaml@main
+    secrets: inherit

.gitignore

@@ -2,6 +2,7 @@
 .idea
 *.class
 *.swp
+.DS_Store
 
 # Contains SQL statements to initialize testing DB with a confidential user and tokens
 # Contains SQL statements to initialize testing DB with a confidential user, assuming they followed the dockstore setup tutorial

README.md

@@ -30,7 +30,7 @@ The following section is useful for users of Dockstore (e.g. those that want to
 launch tools). 
 
 After registering at [dockstore.org](https://dockstore.org), you will be able to download the Dockstore 
-CLI at https://dockstore.org/onboarding
+CLI at [onboarding](https://dockstore.org/onboarding). The Dockstore command line script should be installed in a location in your path.
 
 ### Configuration File
 
@@ -41,12 +41,13 @@ token = <your generated by the dockstore site>
 server-url = https://www.dockstore.org/api
 ```
 
+For developers, if you are working with a custom-built or updated Dockstore client you will need to update the jar in: `~/.dockstore/config/self-installs`.
+
 ### File Provisioning
 
 By default, cwltool reads input files from the local filesystem. Dockstore also adds support for additional file systems
 such as http, https, and ftp. Through a plug-in system, Dockstore also supports 
-the Amazon S3, [Synapse](http://docs.synapse.org/articles/downloading_data.html), and 
-[ICGC Score Client](https://docs.icgc.org/download/guide/#score-client-usage) via [plugins](https://github.com/dockstore).
+Amazon S3 and [Synapse](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html) via [plugins](https://github.com/dockstore).
 
 Download the above set of default plugins via: 
 ```
@@ -68,9 +69,6 @@ cache-dir = /home/<user>/.dockstore/cache   #set this to determine where input f
 
 [dockstore-file-s3-plugin]
 endpoint = #set this to point at a non AWS S3 endpoint
-
-[dockstore-file-icgc-storage-client-plugin]
-client = /media/large_volume/icgc-storage-client-1.0.23/bin/icgc-storage-client
 ```
 
 Additional plugins can be created by taking one of the repos in [plugins](https://github.com/dockstore) as a model and