Rebuilt containers on new base image. #57
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…ce yaml2ped with json2ped. Store the data in the git repo.
…es, jq, gawk, git, wget, and parallel. sha256:a8bdcfc75efe55105958e5b0dfd91aad05284fe334373b17a7aca32bebdc0fd1
…ity functionality.
…iners Create an image preloaded with datasets required for HPO lookup. Relace yaml2ped with json2ped.
Feature: Establish a base image to simplify builds, and move most images to this base.
sha256:a6839c3e35d94c13479d4fd53d6b954fa6df8de3a22399b1e88e2e515f28776f
sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba
sha256:b2165769aedf5548be14bf1aee6f33b86f7a20cb218991887da2f777368c924a
sha256:d70396273c20d74ea3ca05fc9480f9877d1665fdabd12d68423fab6fec5e0eb7
sha256:60f4513e353c293f71c983bd111479b281e4a031a0bb8c00a1a8642bf430781f
sha256:9ca8a2c15739f495f677952bdb99a010c7e7333a3034d28c4d63e5ccf244e4da
sha256:db23f9722ee0cb7770cf944887ea995d9634d20e0be943345f8e3a4fee538ee2
sha256:3c5029aaa38e8a6b0f9b042086691aac3747ccee60045e3e7531ae72059546b2
sha256:82c840a3e3d71769bbd4e21d3ed42e48ff744c10bc12592156114a1922a13f80
- expected input structure for json2ped.py has changed; now expects 1) json array of sample structs and 2) family id as a separate string - string "true"/"false" are now allowed for affected status, in addition to boolean True/False wgs_tertiary sha256:6925e50c6850d8886a9cbe0d984ec8eaea205cca280309820688b60dfc65b1d4
juniper-lake
reviewed
Sep 4, 2024
docker/pbstarphase/Dockerfile
Outdated
| && ln -s /opt/pb-StarPhase-${PBSTARPHASE_VERSION}/data/${CPIC_BUILD_VERSION} /opt/pbstarphase_db.json.gz \ | ||
| && wget https://github.com/PacificBiosciences/pb-StarPhase/releases/download/v${PBSTARPHASE_VERSION}/pbstarphase-v${PBSTARPHASE_VERSION}-x86_64-unknown-linux-gnu.tar.gz \ | ||
| && ln -s /opt/pb-StarPhase-${PBSTARPHASE_VERSION}/data/${CPIC_BUILD_VERSION} /opt/pbstarphase_db.json.gz | ||
| ARG wget https://github.com/PacificBiosciences/pb-StarPhase/releases/download/v${PBSTARPHASE_VERSION}/pbstarphase-v${PBSTARPHASE_VERSION}-x86_64-unknown-linux-gnu.tar.gz \ |
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Yes, and I'm not even sure why this is working.
Updated pbstarphase to 0.14.1 and fixed ARG in Dockerfile.
…-ped Updates to json2ped to allow more flexible input.
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Containers for HumanWGS now share a base image, pb_wdl_base, with tools like samtools, bcftools, htslib, python, jq, etc. Containers for other workflows will be updated in the future.
Smaller python scripts have been moved out of the container and into the WDL using heredocs.