CHANGELOG.md

2.2.6 - 2024-12-04T17:30:49.275803406Z

• Update terra-jupyter-r to 2.2.6
  • Update for R 4.4.2 and Bioc 3.20

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

2.2.5 - 2024-05-15T15:36:28.576892790Z

• Update terra-jupyter-r to 2.2.5
  • Update for R 4.4.0 and Bioc 3.19

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

2.2.4 - 2023-11-14T15:56:44.470211534Z

• Update terra-jupyter-r to 2.2.4
  • Bioconductor 3.18 release

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

2.2.3 - 2023-10-03

• Update terra-jupyter-r to 2.2.3
  • 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-bioconductor:2.2.3

2.2.2 - 2023-07-31

• Update terra-jupyter-r to 2.2.2
  • 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-bioconductor:2.2.2

2.2.1 - 2023-07-06

• Fix bug introduced in https://github.com/DataBiosphere/terra-docker/commit/4a5b4c9212aedcafa2f41fbeb2b161089341c578

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

2.2.0 - 2023-06-23

• Update python 3.7 to 3.10

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

2.1.11 - 2023-06-01T17:49:47.622531112Z

• Update terra-jupyter-r to 2.1.10
  • Bioconductor 3.17 release with R 4.3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.1.11

2.1.10 - 2023-03-13T17:26:34.148443Z

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

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

2.1.9 - 2023-02-09T14:18:48.987542Z

• 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-bioconductor:2.1.9

2.1.8 - 2022-11-22T20:49:44.056023723Z

• Update terra-jupyter-r to 2.1.7
  • Update Bioconductor for 3.16 release

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

2.1.7 - 2022-07-27T13:32:19.884050Z

• Moved AnVIL and supporting packages to be installed in parent image.
• Update terra-jupyter-r to 2.1.6
  • Installs AnVIL and supporting packages.

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

2.1.6 - 2022-07-22

• Fix anvil package install

2.1.5 - 2022-05-20T18:06:39.449113Z

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

2.1.4 - 2022-05-20T18:06:39.449113Z

• reverted, do not use

2.1.3 - 2022-05-20T18:06:39.449113Z

• 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-bioconductor:2.1.3

2.1.2 - 2022-05-17T17:14:41.233909Z

• 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-bioconductor:2.1.2

2.1.1 - 2022-05-10T22:08:25.936576Z

• Update terra-jupyter-base to 1.0.7
  • Install Cromshell 2.0 (https://github.com/broadinstitute/cromshell)

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

2.1.0 - 2022-05-02

• Update terra-jupyter-r to 2.1.0
  • Update Bioconductor to 3.15.0 and R to 4.2.0

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

2.0.6 - 2022-05-02T14:33:23.928899Z

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

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

2.0.5 - 2022-02-02T20:47:42.326830Z

• 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-bioconductor:2.0.5

2.0.4 - 2022-01-06T18:21:41.155891Z

• 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-bioconductor:2.0.4

2.0.3 - 2021-12-14T19:48:03.812081Z

• Update terra-jupyter-r to 2.0.3
  • Update Terra Jupyter image to use latest Bioconductor 3.14

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

2.0.2 - 2021-10-07T14:47:43.359733Z

• Update terra-jupyter-base to 1.0.2
  • Update AsyncMappingKernelManager jupyter/notebook#6164
• Unpinning cwltool version and updating protobuf version to 3.18

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

2.0.1 - 2021-09-10T15:10:44.079307Z

• 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-bioconductor:2.0.1

2.0.0 - 2021-06-09T16:18:53.763986Z

• 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-bioconductor:2.0.0

1.0.15 - 2021-06-07T19:39:55.978624Z

• Update terra-jupyter-r to 1.0.16
  • Update R to 4.1.0 and Bioconductor version to 3.13.

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

1.0.14 - 2021-05-05T16:19:57.470153Z

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

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

1.0.13 - 2021-02-10T00:36:57.149Z

• Update terra-jupyter-r to 1.0.13
  • [IA-2511] Install Seurat R package in terra-jupyter-r image

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

1.0.12 - 2021-01-20T16:00:48.285Z

• 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-bioconductor:1.0.12

1.0.11 - 2020-12-02T17:59:36.375Z

• 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-bioconductor:1.0.11

1.0.10 - 2020-11-16T18:11:40.741594Z

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

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

1.0.9 - 2020-11-04T21:43:54.879Z

• Update terra-jupyter-r to 1.0.9
  • Version upgrades: Bioconductor version 3.12 and R version 4.0.3

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

1.0.8 - 2020-10-26T20:13:57.651Z

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

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

1.0.7 - 2020-10-08T18:42:19.678Z

• 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-bioconductor:1.0.7

1.0.6 - 2020-09-02T15:12:19.845Z

• 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-bioconductor:1.0.6

1.0.5 - 2020-08-18T13:43:26.184Z

• 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-bioconductor:1.0.5

1.0.4 - 07/27/2020

• Update terra-jupyter-r version to 1.0.4

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

1.0.3 - 06/29/2020

• Only user package installations (not image package installations) will persist
• Update terra-jupyter-r version to 1.0.3

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

1.0.2 - 06/26/2020

• Update terra-jupyter-r version to 1.0.2

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

1.0.1 - 06/15/2020

• Update terra-jupyter-r version to 1.0.1

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

1.0.0 - 05/21/2020

• Inherit from terra-jupyter-r:1.0.0.
• This version updates to R-4.0.0 and Bioconductor RELEASE_3_11.
• Update terra-jupyter-bioconductor version to 1.0.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:1.0.0

0.0.15 - 05/18/2020

• Update terra-jupyter-r base image to 0.0.14
  • Adds jupyter notebook extension collapsible headers and code-folding

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.15

0.0.14 - 04/28/2020

• Fix bug in version 0.0.13: switch back to jupyter-user at the end

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.14

0.0.13 - 04/24/2020

• Inherit from terra-jupyter-r:0.0.13
• Remove redundant system libraries.
• Update terra-jupyter-bioconductor version to 0.0.13.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.13

0.0.12 - 02/25/2020

• Update terra-jupyter-r version to 0.0.11
  • Fixes https://broadworkbench.atlassian.net/browse/IA-1676

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.12

0.0.11 - 02/05/2020

• Update terra-jupyter-r base image to 0.0.10
  • Fixes https://broadworkbench.atlassian.net/browse/IA-1653

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.11

0.0.10 - 01/17/2020

• Update terra-jupyter-r version to 0.0.9
• 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-bioconductor:0.0.10

0.0.9 - 12/17/2019

• Upgrade pandas from 0.25.1 to 0.25.3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.9

0.0.8 - 12/11/2019

• Standardize both Jupyter and RStudio Bioconductor package installation.
• Update terra-jupyter-bioconductor version to 0.0.8

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.8

0.0.7 - 11/27/2019

• Use new Bioconductor version 3.10
• Update terra-jupyter-bioconductor version to 0.0.7

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.7

0.0.6 - 11/26/2019

• Fix WORKSPACE_BUCKET environment variable

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.6

0.0.5 - 11/22/2019

• Install AnnotationHub, ExperimentHub, ensembldb, Rtse, scRNAseq, scran.
• Update terra-jupyter-bioconductor version to 0.0.5

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.5

0.0.4 - 11/16/2019

• Update terra-jupyter-r version to 0.0.5
• Remove apt-get upgrade for security purposes

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.4

0.0.3 - 10/18/2019

• Update terra-jupyter-r version to 0.0.3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.3

0.0.2 - 09/04/2019

• Install python packages needed for BiocSklearn, Rcwl.
• Install python3.7-dev for headers required to compile python modules.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.2

0.0.1 - 09/03/2019

• Add system-dependencies needed for terra-jupyter-r image to install Bioconductor packages.
• Install core bioconductor packages to use out of the box.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0.0.1