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CHANGELOG.md

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2.2.6 - 2024-12-04T17:30:49.258285293Z

  • Update for R 4.4.2 and Bioc 3.20

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6

2.2.5 - 2024-05-15T15:36:28.555690376Z

  • Update for R 4.4.0 and Bioc 3.19

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5

2.2.4 - 2023-11-14T15:56:44.443656567Z

  • Bioconductor 3.18 release

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.4

2.2.3 - 2023-10-03

  • Update terra-jupyter-base to 1.1.3
    • Downgrade notebook to 6.5.4 and jupyterlab-server to 2.23.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.3

2.2.2 - 2023-07-31

  • Update terra-jupyter-base to 1.1.2
    • Upgrade Terra Notebook Utils to 0.13.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.2

2.2.1 - 2023-07-06

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.1

2.2.0 - 2023-06-23

  • Python upgrade 3.7 to 3.10

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.0

2.1.10 - 2023-06-01T17:49:47.585402026Z

  • Bioconductor 3.17 release with R 4.3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10

2.1.9 - 2023-03-13T17:26:34.207471Z

  • Update terra-jupyter-base to 1.0.14
    • Include jupyter lab build step

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.9

2.1.8 - 2023-02-09T14:18:49.113028Z

  • Update terra-jupyter-base to 1.0.12
    • Add cloud.google.com gpg key.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.8

2.1.7 - 2022-11-22T20:49:44.016171853Z

  • Update Bioconductor for 3.16 release

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.7

2.1.6 - 2022-07-27T13:32:19.838903Z

  • Installs AnVIL and supporting packages.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.6

2.1.5 - 2022-06-23T10:58:12.961300Z

  • Update terra-jupyter-base to 1.0.10
    • Fix leo_url variable in workspace_cromwell.py script for AoU projects

2.1.4 - 2022-06-23T10:58:12.961300Z

  • reverted, do not use

2.1.3 - 2022-05-20T18:06:39.532374Z

  • Update terra-jupyter-base to 1.0.9
    • Fix adding workspace_cromwell.py script to manage Cromwell App

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.3

2.1.2 - 2022-05-17T17:14:41.312584Z

  • Update terra-jupyter-base to 1.0.8
    • Add script that manages Cromwell app

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.2

2.1.1 - 2022-05-10T22:08:26.010910Z

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.1

2.1.0 - 2022-05-02

  • Update Bioconductor to 3.15.0 and R to 4.2.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.0

2.0.7 - 2022-05-02T14:33:23.994516Z

  • Update terra-jupyter-base to 1.0.6
    • use new nvidia key

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.7

2.0.6 - 2022-04-17

  • Update terra-jupyter-base to 1.0.5
    • Install gcloud alpha storage dependency

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.6

2.0.5 - 2022-02-02T20:47:42.380155Z

  • Update terra-jupyter-base to 1.0.4
    • update notebook_dir to $HOME; install scikit-learn-intelex, xgboost

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.5

2.0.4 - 2022-01-06T18:21:41.216517Z

  • Update terra-jupyter-base to 1.0.3
    • Bumping Google Deeplearning image to 2.7, removing gcc-6 and gcc-8 install due to package problems

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.4

2.0.3 - 2021-12-14T19:48:03.777851Z

  • Update Terra Jupyter image to use latest Bioconductor 3.14

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3

2.0.2 - 2021-10-07T14:47:43.422197Z

  • Update terra-jupyter-base to 1.0.2
  • Unpinning cwltool version and updating protobuf version to 3.18

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2

2.0.1 - 2021-09-10T15:10:44.133967Z

  • Update terra-jupyter-base to 1.0.1
    • Update base image to gcr.io/deeplearning-platform-release/tf2-gpu.2-6 to support TensorFlow 2.6.0
    • Fix multipart Jupyter uploads

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.1

2.0.0 - 2021-06-09T16:18:53.836988Z

  • Update terra-jupyter-base to 1.0.0
    • use gcr.io/deeplearning-platform-release/base-cu110:latest as base

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.0

1.0.15 - 2021-06-07

  • Update R to 4.1.0 and Bioconductor version to 3.13.
  • Update terra-jupyter-r image to 1.0.15

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.15

1.0.14 - 2021-05-05T16:19:57.531117Z

  • Update terra-jupyter-base to 0.0.20
    • [IA-1644] Install crcmod in base image to support GCS composite objects
  • Fix libsbml5 installation

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.14

1.0.13 - 2021-02-10T00:36:57.099Z

  • [IA-2511] Install Seurat R package in terra-jupyter-r image

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.13

1.0.12 - 2021-01-20T16:00:48.341Z

  • Update terra-jupyter-base to 0.0.19
    • [IA-2472] Turn on debug-level logging when JUPYTER_DEBUG_LOGGING env var is true

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.12

1.0.11 - 2020-12-02T17:59:36.434Z

  • Update terra-jupyter-base to 0.0.18
    • bump terra-notebook-utils version to 0.7.0 and move it to base image

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.11

1.0.10 - 2020-11-16T18:11:40.819538Z

  • Update terra-jupyter-base to 0.0.17
    • remove miniconda

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.10

1.0.9 - 2020-11-04T21:43:54.848Z

  • Version upgrades: Bioconductor version 3.12 and R version 4.0.3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.9

1.0.8 - 2020-10-26T20:13:57.736Z

  • Update terra-jupyter-base to 0.0.16
    • add keychain to base image

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.8

1.0.7 - 2020-10-08T18:42:19.728Z

  • Update terra-jupyter-base to 0.0.15
    • include pip binary installation location in PATH

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.7

1.0.6 - 2020-09-02T15:12:19.899Z

  • Update terra-jupyter-base to 0.0.14
    • Terminal now opens to /notebooks directory where PD is mounted

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.6

1.0.5 - 2020-08-18T13:43:26.250Z

  • Update terra-jupyter-base to 0.0.13
    • update notebook to 6.1.1, tornado to 5.1.1

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.5

1.0.4 - 07/27/2020

  • Update terra-jupyter-base image version to 0.0.12

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.4

1.0.3 - 06/29/2020

  • Remove /home/jupyter-user/notebooks/packages from .Renviron file because derived images installed packages should not persist
  • Only user package installations (not image package installations) will persist

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.3

1.0.2 - 06/26/2020

  • Install all image packages as root user
  • remove /home/jupyter-user/.rpackages
  • Add /home/jupyter-user/notebooks/packages so user installed packages persist

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.2

1.0.1 - 06/15/2020

  • Update terra-jupyter-base image version to 0.0.11
  • Add terra-notebook-utils package

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.1

1.0.0 - 05/21/2020

  • Update terra-jupyter-r version to 1.0.0
  • Update R_VERSION to 4.0 and Bioconductor version to release 3.11. Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:1.0.0

0.0.14 - 05/18/2020

  • Update terra-jupyter-base image version to 0.0.10
    • Adds jupyter notebook extension collapsible headers and code-folding Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.14

0.0.13 - 04/23/2020

  • Update terra-jupyter-r version to 0.0.13
  • Change env var names to avoid conflict. Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.13

0.0.12 - 04/15/2020

  • Update terra-jupyter-r version to 0.0.12
  • Install most system dependencies needed for CRAN and Bioconductor packages. Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.12

0.0.11 - 02/25/2020

0.0.10 - 02/05/2020

0.0.9 - 01/17/2020

  • Update terra-jupyter-base version to 0.0.7
  • Make docker image locally runnable with:
    • docker run --rm -it -p 8000:8000 <image>
  • Add FISS library
  • Add OpenJDK 11 Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.9

0.0.8 - 01/15/2020

  • Install reticulate.
  • Update terra-jupyter-r version to 0.0.8 Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.8

0.0.7 - 11/26/2019

  • Update Bioconductor version to 3.10.
  • Fix WORKSPACE_BUCKET environment variable
  • Update terra-jupyter-r version to 0.0.7 Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.7

0.0.6 - 11/22/2019

  • Update make recommended packages updatable.
  • Update terra-jupyter-r version to 0.0.6 Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.6

0.0.5 - 11/16/2019

  • Update terra-jupyter-base version to 0.0.5
  • Remove apt-get upgrade for security purposes Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.5

0.0.4 - 10/18/2019

  • Update terra-jupyter-base version to 0.0.4 Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.4

0.0.3 - 09/03/2019

  • Install all R packages in same location.
  • Make packges updatable with BiocManager::valid() Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.3

0.0.2 - 08/28/2019

  • Add devtools R package
  • Remove spark Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.2

0.0.1 - 08/21/2019

  • Add R 3.6 Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:0.0.1