From ea80649714b1529b9a91a4669a1b0e4f3e0fc178 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 25 Mar 2024 15:54:13 -0400 Subject: [PATCH 1/3] fix: missing WOMtool in prod docker img --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 997cd29..e24676f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN apt-get update -y && \ cp -r vcf2maf/data /opt/data && \ rm -rf vcf2maf -# Install Cromwell + WOMtool +# Download Cromwell + WOMtool ENV CROMWELL_VERSION=86 WORKDIR / RUN curl -L \ @@ -122,8 +122,9 @@ RUN poetry install --without dev # - Copy VCF2MAF COPY --from=downloaded-deps /opt /opt -# - Copy Cromwell +# - Copy Cromwell + WOMtool COPY --from=downloaded-deps /cromwell.jar /cromwell.jar +COPY --from=downloaded-deps /womtool.jar /womtoo.jar # - Copy Ensembl-VEP COPY --from=ensemblorg/ensembl-vep:release_111.0 /usr/share/perl/5.34.0/CPAN /opt/vep From 27b248c1daba7a694717dc9f9ecbad1288acb2ba Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 25 Mar 2024 15:57:07 -0400 Subject: [PATCH 2/3] typo --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e24676f..adf458e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -124,7 +124,7 @@ COPY --from=downloaded-deps /opt /opt # - Copy Cromwell + WOMtool COPY --from=downloaded-deps /cromwell.jar /cromwell.jar -COPY --from=downloaded-deps /womtool.jar /womtoo.jar +COPY --from=downloaded-deps /womtool.jar /womtool.jar # - Copy Ensembl-VEP COPY --from=ensemblorg/ensembl-vep:release_111.0 /usr/share/perl/5.34.0/CPAN /opt/vep From 42561fb7197bb0ca521b0e813a13205ec1137331 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 25 Mar 2024 16:00:44 -0400 Subject: [PATCH 3/3] chore: update lockfile deps --- poetry.lock | 154 ++++++++++++++++++++++++++-------------------------- 1 file changed, 77 insertions(+), 77 deletions(-) diff --git a/poetry.lock b/poetry.lock index a8c1196..2da1993 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "aiofiles" @@ -148,13 +148,13 @@ files = [ [[package]] name = "asgiref" -version = "3.7.2" +version = "3.8.1" description = "ASGI specs, helper code, and adapters" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "asgiref-3.7.2-py3-none-any.whl", hash = "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e"}, - {file = "asgiref-3.7.2.tar.gz", hash = "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed"}, + {file = "asgiref-3.8.1-py3-none-any.whl", hash = "sha256:3e1e3ecc849832fe52ccf2cb6686b7a55f82bb1d6aee72a58826471390335e47"}, + {file = "asgiref-3.8.1.tar.gz", hash = "sha256:c343bd80a0bec947a9860adb4c432ffa7db769836c64238fc34bdc3fec84d590"}, ] [package.dependencies] @@ -195,13 +195,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "bento-lib" -version = "11.5.1" +version = "11.5.2" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = ">=3.10,<4.0" files = [ - {file = "bento_lib-11.5.1-py3-none-any.whl", hash = "sha256:5dfd48a15158dcaa0c0c90f1fd37d60b1a6f7d8fb157780eacc9c7d438a22b33"}, - {file = "bento_lib-11.5.1.tar.gz", hash = "sha256:3b77b292c49a66aa8e9463d550cd38c4d355fbb9863ff598f9084a3ccc7eac77"}, + {file = "bento_lib-11.5.2-py3-none-any.whl", hash = "sha256:a4027469c208028d5456bd747782f485c6b29d17d8d0c80293c60aea48bab21f"}, + {file = "bento_lib-11.5.2.tar.gz", hash = "sha256:bcb5f617df61aab43276ae26e70cbf09498baf490315ff7a180d56e910ca54d8"}, ] [package.dependencies] @@ -218,7 +218,7 @@ werkzeug = ">=2.2.3,<4" [package.extras] asyncpg = ["asyncpg (>=0.29.0,<0.30.0)"] -django = ["django (>=4.2.7,<5)", "djangorestframework (>=3.14.0,<3.15)"] +django = ["django (>=4.2.7,<5.1)", "djangorestframework (>=3.14.0,<3.16)"] fastapi = ["fastapi (>=0.104,<0.111)"] flask = ["flask (>=2.2.5,<4)"] @@ -437,13 +437,13 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "click-didyoumean" -version = "0.3.0" +version = "0.3.1" description = "Enables git-like *did-you-mean* feature in click" optional = false -python-versions = ">=3.6.2,<4.0.0" +python-versions = ">=3.6.2" files = [ - {file = "click-didyoumean-0.3.0.tar.gz", hash = "sha256:f184f0d851d96b6d29297354ed981b7dd71df7ff500d82fa6d11f0856bee8035"}, - {file = "click_didyoumean-0.3.0-py3-none-any.whl", hash = "sha256:a0713dc7a1de3f06bc0df5a9567ad19ead2d3d5689b434768a6145bff77c0667"}, + {file = "click_didyoumean-0.3.1-py3-none-any.whl", hash = "sha256:5c4bb6007cfea5f2fd6583a2fb6701a22a41eb98957e63d0fac41c10e7c3117c"}, + {file = "click_didyoumean-0.3.1.tar.gz", hash = "sha256:4f82fdff0dbe64ef8ab2279bd6aa3f6a99c3b28c05aa09cbfc07c9d7fbb5a463"}, ] [package.dependencies] @@ -497,63 +497,63 @@ files = [ [[package]] name = "coverage" -version = "7.4.3" +version = "7.4.4" description = "Code coverage measurement for Python" optional = false 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