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2.3.8 - 2024-09-04

  • Update terra-jupyter-python to 1.1.6
  • Update terra-jupyter-r to 2.2.6
    • Update terra-jupyter-base to 1.1.4
      • Update terra-notebook-utils to 0.14.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8

2.3.7 - 2024-05-15T15:36:28.602743427Z

  • 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-gatk:2.3.7

2.3.6 - 2023-11-27

  • Update Samtools to 1.18
  • Update terra-jupyter-python to 2.2.5

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.6

2.3.5 - 2023-11-14T15:56:44.486168932Z

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

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.5

2.3.4 - 2023-10-06

  • Update terra-jupyter-python to 1.1.4
    • Downgrade pytz to 2023.3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.4

2.3.3 - 2023-10-03

  • Update terra-jupyter-r to 2.2.3
  • Update terra-jupyter-python to 1.1.3
    • 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-gatk:2.3.3

2.3.2 - 2023-07-31

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

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.2

2.3.1 - 2023-07-28

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.1

2.3.0 - 2023-06-23

  • Update python 3.7 to 3.10

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.0

2.2.14 - 2023-06-09

  • Actually install bedtools to accessible path

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.14

2.2.13 - 2023-06-01T17:49:47.668283846Z

  • 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-gatk:2.2.13

2.2.12 - 2023-05-31T13:55:05

  • Add bcftools
  • Add bedtools

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.12

2.2.11 - 2023-03-13T17:26:34.219509Z

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

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.11

2.2.10 - 2023-02-09T14:18:49.138553Z

  • 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-gatk:2.2.10

2.2.9 - 2022-11-22T20:49:44.110597220Z

  • 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-gatk:2.2.9

2.2.8 - 2022-07-27T13:32:19.939107Z

  • Update terra-jupyter-r to 2.1.6
    • Installs AnVIL and supporting packages.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.8

2.2.7 - 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

2.2.6 - 2022-06-23T10:58:12.961300Z

  • reverted, do not use

2.2.5 - 2022-06-09

  • Improve Python package matching from -python image. No longer causes downstream issues on package uninstall.

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

2.2.4 - 2022-06-03T18:35:22.539434Z

  • reverted, do not use

2.2.3 - 2022-05-20T18:06:39.552362Z

  • 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-gatk:2.2.3

2.2.2 - 2022-05-17T17:14:41.328568Z

  • 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-gatk:2.2.2

2.2.1 - 2022-05-10T22:08:26.027031Z

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

2.2.0 - 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-gatk:2.2.0

2.1.0 - 2022-05-02T14:33:24.006107Z

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

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

2.0.9 - 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-gatk:2.0.9

2.0.8 - 2022-02-02T20:47:42.389262Z

  • 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-gatk:2.0.8

2.0.7 - 2022-01-06T18:21:41.225176Z

  • 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-gatk:2.0.7

2.0.6 - 2021-12-14T19:48:03.830678Z

  • 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-gatk:2.0.6

2.0.5 - 2021-12-15T18:29:12.526374Z

  • Upgrade gatk image to 4.2.4.0

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

2.0.4 - 2021-10-07T14:47:43.431586Z

  • 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-gatk:2.0.4

2.0.3 - 2021-09-23

  • [SUP-465] Terra base gatk notebook image needs Python dependencies
    • Added GATK Python Package install
    • Apply Patch for CNNScoreVariant bug

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

2.0.2 - 2021-09-10T15:10:44.143280Z

  • 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-gatk:2.0.2

2.0.1 - 2021-07-12

  • Upgrade gatk version to 4.2.0.0

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

2.0.0 - 2021-06-09T16:18:53.850703Z

  • 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-gatk:2.0.0

1.1.3 - 2021-06-07T19:39:55.994874Z

  • 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-gatk:1.1.3

1.1.2 - 2021-05-05T16:19:57.539858Z

  • 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-gatk:1.1.2

1.1.1 - 2021-04-05T17:29:05.428Z

  • Update terra-jupyter-python to 0.1.1
    • fix ggplot import bug

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:1.1.1

1.1.0 - 2021-03-20

  • Update terra-jupyter-python to 0.1.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:1.1.0

1.0.15 - 2021-02-10T00:36:57.172Z

  • 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-gatk:1.0.15

1.0.14 - 2021-01-20T16:00:48.352Z

  • 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-gatk:1.0.14

1.0.13 - 2020-12-09T18:50:57.311Z

  • Update terra-jupyter-python to 0.0.22
    • [IA-2420] Update to a newer version of pymc3

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

1.0.12 - 2020-12-02T17:59:36.443Z

  • 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-gatk:1.0.12

1.0.11 - 2020-11-16T18:11:40.830329Z

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

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

1.0.10 - 2020-11-10T13:26:19.126Z

  • Update terra-jupyter-python to 0.0.19
    • Remove Python package enum34. Fixes #175

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

1.0.9 - 2020-11-04T21:43:54.895Z

  • 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-gatk:1.0.9

1.0.8 - 2020-10-26T20:13:57.750Z

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

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

1.0.7 - 2020-10-08T18:42:19.735Z

  • 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-gatk:1.0.7

1.0.6 - 2020-09-02T15:12:19.908Z

  • 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-gatk:1.0.6

1.0.5 - 2020-08-18T13:43:26.263Z

  • 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-gatk:1.0.5

1.0.4 - 07/27/2020

  • Update terra-jupyter-r to 1.0.4
  • Update terra-jupyter-python to 0.0.14

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

1.0.1 - 06/15/2020

  • Update terra-jupyter-python base image to 0.0.32 and terra-jupyter-r base image to 1.0.1

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

1.0.0 - 05/21/2020

  • Update terra-jupyter-r base image to 1.0.0

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

0.0.16 - 05/18/2020

  • Update terra-jupyter-python base image to 0.0.12 and 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-gatk:0.0.16

0.0.15 - 04/28/2020

  • Update terra-jupyter-python base image to 0.0.11
    • Add Google Cloud support to pysam

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

0.0.14 - 04/24/2020

  • Update terra-jupyter-r version to 0.0.13
  • Update terra-jupyter-gatk version to 0.0.14

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

0.0.13 - 02/26/2020

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

0.0.12 - 02/25/2020

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

0.0.11 - 02/05/2020

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

0.0.10 - 01/17/2020

  • Update terra-jupyter-python version to 0.0.8
  • Update terra-jupyter-r version to 0.0.9
  • Make docker image locally runnable with:
    • docker run --rm -it -p 8000:8000 <image>
  • Remove default-jre and default-jdk since they are now provided in the base image

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:0.0.10

0.0.9 - 1/15/2020

  • Update terra-jupyter-python version to 0.0.7
  • Update terra-jupyter-r version to 0.0.8

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

0.0.8 - 1/11/2020

  • Upgrade GATK version to 4.1.4.1

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

0.0.7 - 1/2/2020

  • Upgrade terra-jupyter-python version

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

0.0.5 - 11/22/2019

  • Update terra-jupyter-r version to 0.0.6

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

0.0.4 - 11/16/2019

  • Update terra-jupyter-r version to 0.0.5
  • Update terra-jupyter-python version to 0.0.4
  • Remove apt-get upgrade for security purposes

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

0.0.3 - 10/18/2019

  • Update terra-jupyter-r version to 0.0.4

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

0.0.2 - 10/10/2019

Use version 0.0.2 of python image

0.0.1 - 09/24/2019

  • added all from terra-jupyter-python:0.0.1
  • added all from terra-jupyter-r:0.0.3
  • added Open JDK
  • added GATK 4.1.3.0
  • added Samtools