New DataSHIELD analysis packages profiles #17
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Pull Request Overview
This PR introduces two new DataSHIELD analysis package profiles (quebrada-lamda and quebrada-lamda-permissive) and updates existing profiles to newer versions with package dependency updates.
- Adds complete directory structures for quebrada-lamda and quebrada-lamda-permissive profiles with Docker configurations, build files, and documentation
- Updates omicron-karma profiles from version 1.0.0 to devel with base image and package version updates
- Updates margin-idiom profiles from version 1.2.6 to 2.1.1 with new dsCoda package and reordered installations
Reviewed Changes
Copilot reviewed 24 out of 24 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| quebrada-lamda/docker-compose.yml | Docker compose configuration for new quebrada-lamda profile |
| quebrada-lamda/README.md | Documentation for new quebrada-lamda profile |
| quebrada-lamda/Makefile | Build automation for quebrada-lamda Docker images |
| quebrada-lamda/LICENSE | GPL v3 license for quebrada-lamda profile |
| quebrada-lamda/Dockerfile | Docker image definition extending rock-base:6.3.4-R4.5.2 |
| quebrada-lamda-permissive/docker-compose.yml | Docker compose configuration for permissive variant |
| quebrada-lamda-permissive/README.md | Documentation for permissive variant |
| quebrada-lamda-permissive/Makefile | Build automation for permissive variant |
| quebrada-lamda-permissive/LICENSE | GPL v3 license for permissive variant |
| quebrada-lamda-permissive/Dockerfile | Extends quebrada-lamda with permissive dsBase version |
| omicron-karma/docker-compose.yml | Updates image tag from 1.0.0 to devel |
| omicron-karma/Makefile | Updates version tag to devel |
| omicron-karma/Dockerfile | Updates base image to 6.3.4 and dsBase to v6.3.4 |
| omicron-karma-permissive/docker-compose.yml | Updates image tag from draft to devel |
| omicron-karma-permissive/Makefile | Updates version tag to devel |
| omicron-karma-permissive/Dockerfile | Updates base image reference and dsBase to v6.3.4-dev-permissive |
| margin-idiom/docker-compose.yml | Updates image tag from 1.2.6 to 2.1.1 |
| margin-idiom/Makefile | Updates version tag to 2.1.1 |
| margin-idiom/Dockerfile | Updates base image, adds dsCoda package, reorders installations, updates dsBase to v6.3.5-dev |
| margin-idiom-persistent/docker-compose.yml | Updates image tag to 2.1.1 |
| margin-idiom-persistent/Makefile | Updates version tag to 2.1.1 |
| margin-idiom-persistent/Dockerfile | Updates base image reference and dsBase version |
| lemon-donkey/Dockerfile | Updates base image from 6.3.1-R4.4.2 to 6.3.3, updates package versions |
| lemon-donkey-permissive/Dockerfile | Updates dsBase version to 6.3.4-RC5-permissive |
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| FROM datashield/rock-lemon-donkey:draft | ||
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| ENV DSBASE_VERSION=v6.3.1-permissive | ||
| ENV DSBASE_VERSION=6.3.4-RC5-permissive |
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Inconsistent version format: DSBASE_VERSION uses 6.3.4-RC5-permissive without the v prefix. While the base version in lemon-donkey also lacks the prefix, consider adding v for consistency with other DataSHIELD version patterns (e.g., v6.3.4-RC5-permissive).
Suggested change
| ENV DSBASE_VERSION=6.3.4-RC5-permissive | |
| ENV DSBASE_VERSION=v6.3.4-RC5-permissive |
| @@ -0,0 +1,3 @@ | |||
| # docker-rock-quebrada-lamda | |||
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| [Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [quebrada-lamda](https://datashield.org/help/standard-profiles-and-plaforms). | |||
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Typo in URL: "plaforms" should be "platforms".
Suggested change
| [Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [quebrada-lamda](https://datashield.org/help/standard-profiles-and-plaforms). | |
| [Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [quebrada-lamda](https://datashield.org/help/standard-profiles-and-platforms). |
| @@ -0,0 +1,3 @@ | |||
| # docker-rock-quebrada-lamda-permissive | |||
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| [Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [quebrada-lamda-permissive](https://datashield.org/help/standard-profiles-and-plaforms). | |||
There was a problem hiding this comment.
Typo in URL: "plaforms" should be "platforms".
Suggested change
| [Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [quebrada-lamda-permissive](https://datashield.org/help/standard-profiles-and-plaforms). | |
| [Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [quebrada-lamda-permissive](https://datashield.org/help/standard-profiles-and-platforms). |
| ENV DSMTL_VERSION=0.9.9 | ||
| ENV DSSURVIVAL_VERSION=v2.1.3 | ||
| ENV DSBASE_VERSION=6.3.3 | ||
| ENV DSBASE_VERSION=v6.3.4 |
There was a problem hiding this comment.
Inconsistent version format: DSBASE_VERSION uses 6.3.3 without the v prefix, while other version variables in the file use the v prefix (e.g., v2.1.3, v1.0.18-2). Consider using v6.3.3 for consistency.
| ENV DSMTL_VERSION=0.9.9 | ||
| ENV DSSURVIVAL_VERSION=v2.1.3 | ||
| ENV DSBASE_VERSION=6.3.1 | ||
| ENV DSBASE_VERSION=6.3.4-RC5 |
There was a problem hiding this comment.
Inconsistent version format: DSBASE_VERSION uses 6.3.4-RC5 without the v prefix, while other version variables in the file use the v prefix (e.g., v2.1.3, v1.0.18-2, v1.0.4). Consider using v6.3.4-RC5 for consistency.
Suggested change
| ENV DSBASE_VERSION=6.3.4-RC5 | |
| ENV DSBASE_VERSION=v6.3.4-RC5 |
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