diff --git a/.gitignore b/.gitignore index 5bc1f379d..9be685cad 100644 --- a/.gitignore +++ b/.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 diff --git a/README.md b/README.md index 3fc2b0dc5..42d11b827 100644 --- a/README.md +++ b/README.md @@ -45,8 +45,7 @@ server-url = https://www.dockstore.org/api 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: ``` diff --git a/circle_ci_test_data.zip.enc b/circle_ci_test_data.zip.enc index 091f69b89..d04721a4e 100644 Binary files a/circle_ci_test_data.zip.enc and b/circle_ci_test_data.zip.enc differ diff --git a/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml b/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml index 60281d248..06f3c1b96 100644 --- a/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml +++ b/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml @@ -36,7 +36,7 @@ io.dockstore dockstore-integration-testing - 1.15.0-rc.1 + 1.15.4-alpha.2 tests compile @@ -49,13 +49,13 @@ io.dockstore dockstore-common - 1.15.0-rc.1 + 1.15.4-alpha.2 compile io.dockstore dockstore-webservice - 1.15.0-rc.1 + 1.15.4-alpha.2 compile @@ -67,7 +67,7 @@ io.dockstore openapi-java-client - 1.15.0-rc.1 + 1.15.4-alpha.2 compile diff --git a/dockstore-cli-reports/generated/src/main/resources/pom.xml b/dockstore-cli-reports/generated/src/main/resources/pom.xml index 217e4c97b..a7c6917c8 100644 --- a/dockstore-cli-reports/generated/src/main/resources/pom.xml +++ b/dockstore-cli-reports/generated/src/main/resources/pom.xml @@ -30,13 +30,13 @@ io.dockstore dockstore-webservice - 1.15.0-rc.1 + 1.15.4-alpha.2 compile io.dockstore dockstore-common - 1.15.0-rc.1 + 1.15.4-alpha.2 compile diff --git a/dockstore-client/generated/src/main/resources/pom.xml b/dockstore-client/generated/src/main/resources/pom.xml index 0c201c3a7..f9af8469e 100644 --- a/dockstore-client/generated/src/main/resources/pom.xml +++ b/dockstore-client/generated/src/main/resources/pom.xml @@ -66,7 +66,7 @@ io.dockstore dockstore-common - 1.15.0-rc.1 + 1.15.4-alpha.2 compile @@ -78,7 +78,7 @@ io.dockstore openapi-java-client - 1.15.0-rc.1 + 1.15.4-alpha.2 compile diff --git a/pom.xml b/pom.xml index 08d4e1578..c59ead80e 100644 --- a/pom.xml +++ b/pom.xml @@ -38,7 +38,7 @@ scm:git:git@github.com:dockstore/dockstore-cli.git UTF-8 - 1.15.0-rc.1 + 1.15.4-alpha.2 2.22.2 2.22.2 false diff --git a/scripts/install-tests.sh b/scripts/install-tests.sh index f14c54c43..147fa7f36 100755 --- a/scripts/install-tests.sh +++ b/scripts/install-tests.sh @@ -14,7 +14,7 @@ fi if [ "${TESTING_PROFILE}" = "toil-integration-tests" ]; then pip3 install --user toil[cwl]==3.15.0 else - pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/develop/dockstore-webservice/src/main/resources/requirements/1.14.0/requirements3.txt + pip3 install --user -r https://raw.githubusercontent.com/dockstore/dockstore/hotfix/1.15.4/dockstore-webservice/src/main/resources/requirements/1.15.0/requirements3.txt fi if [ "${TESTING_PROFILE}" = "singularity-tests" ]; then