From 2d69a71e7496baf6f116a66255c8d4db0d9fe993 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Fri, 26 May 2023 13:53:46 -0400 Subject: [PATCH 01/13] Add skera image --- docker/skera/Dockerfile | 18 ++++++++++++++++++ docker/skera/build.env | 6 ++++++ 2 files changed, 24 insertions(+) create mode 100644 docker/skera/Dockerfile create mode 100644 docker/skera/build.env diff --git a/docker/skera/Dockerfile b/docker/skera/Dockerfile new file mode 100644 index 0000000..d322c20 --- /dev/null +++ b/docker/skera/Dockerfile @@ -0,0 +1,18 @@ +FROM ubuntu:focal + +MAINTAINER Heather Ward + +ARG IMAGE_NAME +ENV IMAGE_NAME "${IMAGE_NAME}" +ARG IMAGE_TAG +ENV IMAGE_TAG "${IMAGE_TAG}" + +RUN apt-get -qq update \ + && apt-get -qq install \ + wget \ + && rm -rf /var/lib/apt/lists/* + +ARG SKERA_VERSION +RUN wget https://github.com/PacificBiosciences/skera/releases/download/v${SKERA_VERSION}/skera --directory-prefix /opt/skera \ + && chmod +x /opt/skera/skera \ + && ln -s /opt/skera/skera /usr/local/bin diff --git a/docker/skera/build.env b/docker/skera/build.env new file mode 100644 index 0000000..cd5f12b --- /dev/null +++ b/docker/skera/build.env @@ -0,0 +1,6 @@ +# Tool versions +SKERA_VERSION=0.1.0 + +# Image info +IMAGE_NAME=skera +IMAGE_TAG=${SKERA_VERSION} From 2fb1fa61a308853996444483f3ef496d05f01696 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Fri, 26 May 2023 16:52:53 -0400 Subject: [PATCH 02/13] Add isoseq3 docker --- docker/isoseq3/Dockerfile | 18 ++++++++++++++++++ docker/isoseq3/build.env | 6 ++++++ 2 files changed, 24 insertions(+) create mode 100644 docker/isoseq3/Dockerfile create mode 100644 docker/isoseq3/build.env diff --git a/docker/isoseq3/Dockerfile b/docker/isoseq3/Dockerfile new file mode 100644 index 0000000..9c22f59 --- /dev/null +++ b/docker/isoseq3/Dockerfile @@ -0,0 +1,18 @@ +FROM ubuntu:focal + +MAINTAINER Heather Ward + +ARG IMAGE_NAME +ENV IMAGE_NAME "${IMAGE_NAME}" +ARG IMAGE_TAG +ENV IMAGE_TAG "${IMAGE_TAG}" + +RUN apt-get -qq update \ + && apt-get -qq install \ + wget \ + && rm -rf /var/lib/apt/lists/* + +ARG ISOSEQ3_VERSION +RUN wget https://github.com/PacificBiosciences/IsoSeq/releases/download/v${ISOSEQ3_VERSION}/isoseq3 --directory-prefix /opt/isoseq3 \ + && chmod +x /opt/isoseq3/isoseq3 \ + && ln -s /opt/isoseq3/isoseq3 /usr/local/bin diff --git a/docker/isoseq3/build.env b/docker/isoseq3/build.env new file mode 100644 index 0000000..d00ca9e --- /dev/null +++ b/docker/isoseq3/build.env @@ -0,0 +1,6 @@ +# Tool versions +ISOSEQ3_VERSION=3.8.2 + +# Image info +IMAGE_NAME=isoseq3 +IMAGE_TAG=${ISOSEQ3_VERSION} From c9bd21b9cab3cc87f1afd21b118e3fb3839d6fcc Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Mon, 29 May 2023 16:53:00 -0400 Subject: [PATCH 03/13] Make an updated version of lima for isoseq Version 2.5.0, used in TargetEnrichment, does not add the SOURCE field to the RG for segmented reads; this is fixed in v2.7.1. --- docker/lima/isoseq/Dockerfile | 21 ++++++++++++++++++++ docker/lima/isoseq/build.env | 6 ++++++ docker/lima/{ => targetenrichment}/build.env | 2 +- 3 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 docker/lima/isoseq/Dockerfile create mode 100644 docker/lima/isoseq/build.env rename docker/lima/{ => targetenrichment}/build.env (75%) diff --git a/docker/lima/isoseq/Dockerfile b/docker/lima/isoseq/Dockerfile new file mode 100644 index 0000000..79cf1ad --- /dev/null +++ b/docker/lima/isoseq/Dockerfile @@ -0,0 +1,21 @@ +FROM ubuntu:focal + +MAINTAINER Heather Ward + +ARG IMAGE_NAME +ENV IMAGE_NAME "${IMAGE_NAME}" +ARG IMAGE_TAG +ENV IMAGE_TAG "${IMAGE_TAG}" + +RUN apt-get -qq update \ + && apt-get -qq install \ + wget \ + && rm -rf /var/lib/apt/lists/* + +ARG LIMA_VERSION +RUN wget https://github.com/PacificBiosciences/barcoding/releases/download/v${LIMA_VERSION}/lima.tar.gz \ + && mkdir /opt/lima \ + && tar -zxvf lima.tar.gz --directory /opt/lima \ + && rm lima.tar.gz + +ENV PATH ${PATH}:/opt/lima diff --git a/docker/lima/isoseq/build.env b/docker/lima/isoseq/build.env new file mode 100644 index 0000000..4c6a150 --- /dev/null +++ b/docker/lima/isoseq/build.env @@ -0,0 +1,6 @@ +# Tool versions +LIMA_VERSION=2.7.1 + +# Image info +IMAGE_NAME=lima +IMAGE_TAG=${LIMA_VERSION} diff --git a/docker/lima/build.env b/docker/lima/targetenrichment/build.env similarity index 75% rename from docker/lima/build.env rename to docker/lima/targetenrichment/build.env index d1d5c90..e91d2da 100644 --- a/docker/lima/build.env +++ b/docker/lima/targetenrichment/build.env @@ -5,4 +5,4 @@ CONDA_ENVIRONMENT_REPO_HASH=8e6261b IMAGE_NAME=lima IMAGE_TAG=${CONDA_ENVIRONMENT_REPO_HASH} CONDA_ENVIRONMENT=${IMAGE_NAME} -DOCKERFILE=../Conda_dockerfile_TargetEnrichment +DOCKERFILE=../../Conda_dockerfile_TargetEnrichment From 4c6b58734b76815f4b6242beb36c2d17dc282c50 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Tue, 30 May 2023 10:39:44 -0400 Subject: [PATCH 04/13] Add samtools docker --- docker/samtools/isoseq/Dockerfile | 27 +++++++++++++++++++++++++++ docker/samtools/isoseq/build.env | 6 ++++++ 2 files changed, 33 insertions(+) create mode 100644 docker/samtools/isoseq/Dockerfile create mode 100644 docker/samtools/isoseq/build.env diff --git a/docker/samtools/isoseq/Dockerfile b/docker/samtools/isoseq/Dockerfile new file mode 100644 index 0000000..036d8c5 --- /dev/null +++ b/docker/samtools/isoseq/Dockerfile @@ -0,0 +1,27 @@ +FROM ubuntu:focal + +MAINTAINER Heather Ward + +ARG IMAGE_NAME +ENV IMAGE_NAME "${IMAGE_NAME}" +ARG IMAGE_TAG +ENV IMAGE_TAG "${IMAGE_TAG}" + +RUN apt-get -qq update \ + && apt-get -qq install \ + wget \ + build-essential \ + zlib1g-dev \ + libncurses5-dev \ + liblzma-dev \ + libbz2-dev \ + libcurl4-openssl-dev \ + && rm -rf /var/lib/apt/lists/* + +ARG SAMTOOLS_VERSION +RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \ + && tar -jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 --directory /opt \ + && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 +RUN cd /opt/samtools-${SAMTOOLS_VERSION} \ + && make \ + && make install diff --git a/docker/samtools/isoseq/build.env b/docker/samtools/isoseq/build.env new file mode 100644 index 0000000..1ea69a7 --- /dev/null +++ b/docker/samtools/isoseq/build.env @@ -0,0 +1,6 @@ +# Tool versions +SAMTOOLS_VERSION=1.17 + +# Image info +IMAGE_NAME=samtools +IMAGE_TAG=${SAMTOOLS_VERSION} From b9354e0dcb220fb65c777bcaff19f17038f262f1 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Tue, 30 May 2023 11:51:31 -0400 Subject: [PATCH 05/13] Add pigeon docker --- docker/pigeon/Dockerfile | 18 ++++++++++++++++++ docker/pigeon/build.env | 6 ++++++ 2 files changed, 24 insertions(+) create mode 100644 docker/pigeon/Dockerfile create mode 100644 docker/pigeon/build.env diff --git a/docker/pigeon/Dockerfile b/docker/pigeon/Dockerfile new file mode 100644 index 0000000..9aa0d77 --- /dev/null +++ b/docker/pigeon/Dockerfile @@ -0,0 +1,18 @@ +FROM ubuntu:focal + +MAINTAINER Heather Ward + +ARG IMAGE_NAME +ENV IMAGE_NAME "${IMAGE_NAME}" +ARG IMAGE_TAG +ENV IMAGE_TAG "${IMAGE_TAG}" + +RUN apt-get -qq update \ + && apt-get -qq install \ + wget \ + && rm -rf /var/lib/apt/lists/* + +ARG PIGEON_VERSION +RUN wget https://github.com/PacificBiosciences/pigeon/releases/download/v${PIGEON_VERSION}/pigeon --directory-prefix /opt/pigeon \ + && chmod +x /opt/pigeon/pigeon \ + && ln -s /opt/pigeon/pigeon /usr/local/bin diff --git a/docker/pigeon/build.env b/docker/pigeon/build.env new file mode 100644 index 0000000..993773a --- /dev/null +++ b/docker/pigeon/build.env @@ -0,0 +1,6 @@ +# Tool versions +PIGEON_VERSION=1.0.0 + +# Image info +IMAGE_NAME=pigeon +IMAGE_TAG=${PIGEON_VERSION} From e8258518dfb8fb1a3053c284ea4aa81ab8d8c0aa Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Wed, 31 May 2023 13:35:21 -0400 Subject: [PATCH 06/13] Add pbbam docker --- docker/pbbam/build.env | 9 +++++++++ docker/pbbam/pbbam.template.yaml | 4 ++++ 2 files changed, 13 insertions(+) create mode 100644 docker/pbbam/build.env create mode 100644 docker/pbbam/pbbam.template.yaml diff --git a/docker/pbbam/build.env b/docker/pbbam/build.env new file mode 100644 index 0000000..7335f25 --- /dev/null +++ b/docker/pbbam/build.env @@ -0,0 +1,9 @@ +# Tool versions +PBBAM_VERSION=1.6.0 + +# Image info +IMAGE_NAME=pbbam +IMAGE_TAG=${PBBAM_VERSION} +CONDA_ENVIRONMENT=${IMAGE_NAME} +CONDA_ENVIRONMENT_TEMPLATE=${IMAGE_NAME}.template.yaml +DOCKERFILE=../Conda_dockerfile diff --git a/docker/pbbam/pbbam.template.yaml b/docker/pbbam/pbbam.template.yaml new file mode 100644 index 0000000..b637870 --- /dev/null +++ b/docker/pbbam/pbbam.template.yaml @@ -0,0 +1,4 @@ +channels: + - bioconda +dependencies: + - pbbam==${PBBAM_VERSION} \ No newline at end of file From 8db45ee562729ad7e5efdd6d2b8d37f69343abff Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Mon, 12 Jun 2023 18:06:54 -0400 Subject: [PATCH 07/13] Add pbbam version 2.1.0 --- docker/Conda_dockerfile | 19 ------- docker/pbbam/Dockerfile | 86 ++++++++++++++++++++++++++++++++ docker/pbbam/build.env | 11 ++-- docker/pbbam/pbbam.template.yaml | 4 -- 4 files changed, 93 insertions(+), 27 deletions(-) delete mode 100644 docker/Conda_dockerfile create mode 100644 docker/pbbam/Dockerfile delete mode 100644 docker/pbbam/pbbam.template.yaml diff --git a/docker/Conda_dockerfile b/docker/Conda_dockerfile deleted file mode 100644 index d988896..0000000 --- a/docker/Conda_dockerfile +++ /dev/null @@ -1,19 +0,0 @@ -FROM continuumio/miniconda3:4.12.0 - -MAINTAINER Heather Ward - -ARG IMAGE_NAME -ENV IMAGE_NAME "${IMAGE_NAME}" -ARG IMAGE_TAG -ENV IMAGE_TAG "${IMAGE_TAG}" -ARG CONDA_ENVIRONMENT -ENV CONDA_ENVIRONMENT "${CONDA_ENVIRONMENT}" - -COPY "${CONDA_ENVIRONMENT}.populated.yaml" scripts* /opt/scripts/ - -RUN mkdir /opt/envs && \ - mv "/opt/scripts/${CONDA_ENVIRONMENT}.populated.yaml" "/opt/envs/${CONDA_ENVIRONMENT}.yaml" && \ - conda env create --file "/opt/envs/${CONDA_ENVIRONMENT}.yaml" --name "${CONDA_ENVIRONMENT}" -ENV PATH /opt/conda/envs/${CONDA_ENVIRONMENT}/bin:/opt/scripts:$PATH - -RUN echo "source activate ${CONDA_ENVIRONMENT}" >> ~/.bashrc diff --git a/docker/pbbam/Dockerfile b/docker/pbbam/Dockerfile new file mode 100644 index 0000000..4841774 --- /dev/null +++ b/docker/pbbam/Dockerfile @@ -0,0 +1,86 @@ +FROM ubuntu:focal + +MAINTAINER Heather Ward + +ARG IMAGE_NAME +ENV IMAGE_NAME "${IMAGE_NAME}" +ARG IMAGE_TAG +ENV IMAGE_TAG "${IMAGE_TAG}" + +ENV DEBIAN_FRONTEND noninteractive +RUN apt-get -qq update \ + && apt-get -qq install \ + wget \ + unzip \ + python-dev \ + python3-pip \ + zlib1g-dev \ + libncurses5-dev \ + liblzma-dev \ + libbz2-dev \ + libcurl4-openssl-dev \ + libgtest-dev \ + pkg-config \ + git \ + cmake \ + && rm -rf /var/lib/apt/lists/* + +# Need bash for curly brace pattern replace for boost version +SHELL ["/bin/bash", "-c"] +ARG BOOST_VERSION +RUN wget https://boostorg.jfrog.io/artifactory/main/release/${BOOST_VERSION}/source/boost_${BOOST_VERSION//./_}.tar.gz \ + && tar -zxvf boost_${BOOST_VERSION//./_}.tar.gz --directory /opt \ + && rm boost_${BOOST_VERSION//./_}.tar.gz +RUN cd /opt/boost_${BOOST_VERSION//./_} \ + && ./bootstrap.sh \ + && ./b2 \ + && ./b2 headers \ + && ./b2 install + +ARG MESON_VERSION +RUN python3 -m pip install meson==${MESON_VERSION} cram + +ARG HTSLIB_VERSION +RUN wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 \ + && tar -jxvf htslib-${HTSLIB_VERSION}.tar.bz2 --directory /opt \ + && rm htslib-${HTSLIB_VERSION}.tar.bz2 +RUN cd /opt/htslib-${HTSLIB_VERSION} \ + && make \ + && make install + +ARG SAMTOOLS_VERSION +RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \ + && tar -jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 --directory /opt \ + && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 +RUN cd /opt/samtools-${SAMTOOLS_VERSION} \ + && make \ + && make install + +ARG NINJA_VERSION +RUN mkdir /opt/ninja \ + && wget https://github.com/ninja-build/ninja/releases/download/v${NINJA_VERSION}/ninja-linux.zip \ + && unzip -d /opt/ninja ninja-linux.zip \ + && rm ninja-linux.zip \ + && ln -s /opt/ninja/ninja /usr/local/bin/ninja + +ARG PBCOPPER_VERSION +RUN wget https://github.com/PacificBiosciences/pbcopper/archive/refs/tags/v${PBCOPPER_VERSION}.tar.gz \ + && tar -zxvf v${PBCOPPER_VERSION}.tar.gz --directory /opt \ + && rm v${PBCOPPER_VERSION}.tar.gz +RUN cd /opt/pbcopper-${PBCOPPER_VERSION} \ + && meson build . \ + && cd build \ + && meson install + +ARG PBBAM_VERSION +RUN wget https://github.com/PacificBiosciences/pbbam/archive/refs/tags/v${PBBAM_VERSION}.tar.gz \ + && tar -zxvf v${PBBAM_VERSION}.tar.gz --directory /opt \ + && rm v${PBBAM_VERSION}.tar.gz +# Workaround for "error: ‘ssize’ is not a member of ‘std’; did you mean ‘size’?" +RUN cd /opt/pbbam-2.1.0 \ + && sed -i 's~std::ssize~std::size~g' src/PbiFilterTypes.cpp \ + && meson build . \ + && cd build \ + && meson install + +ENV LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib/x86_64-linux-gnu/ diff --git a/docker/pbbam/build.env b/docker/pbbam/build.env index 7335f25..cc154ff 100644 --- a/docker/pbbam/build.env +++ b/docker/pbbam/build.env @@ -1,9 +1,12 @@ # Tool versions -PBBAM_VERSION=1.6.0 +PBBAM_VERSION=2.1.0 +BOOST_VERSION=1.82.0 +MESON_VERSION=0.57.0 +HTSLIB_VERSION=1.17 +SAMTOOLS_VERSION=1.17 +NINJA_VERSION=1.11.1 +PBCOPPER_VERSION=2.0.0 # Image info IMAGE_NAME=pbbam IMAGE_TAG=${PBBAM_VERSION} -CONDA_ENVIRONMENT=${IMAGE_NAME} -CONDA_ENVIRONMENT_TEMPLATE=${IMAGE_NAME}.template.yaml -DOCKERFILE=../Conda_dockerfile diff --git a/docker/pbbam/pbbam.template.yaml b/docker/pbbam/pbbam.template.yaml deleted file mode 100644 index b637870..0000000 --- a/docker/pbbam/pbbam.template.yaml +++ /dev/null @@ -1,4 +0,0 @@ -channels: - - bioconda -dependencies: - - pbbam==${PBBAM_VERSION} \ No newline at end of file From 6b3819b6bd7861e2e7644572b7ca36216929b306 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Tue, 13 Jun 2023 10:42:55 -0400 Subject: [PATCH 08/13] Upgrade to g++-11 for access to c++ stdlib 20 --- docker/pbbam/Dockerfile | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/docker/pbbam/Dockerfile b/docker/pbbam/Dockerfile index 4841774..eaca09b 100644 --- a/docker/pbbam/Dockerfile +++ b/docker/pbbam/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:focal +FROM ubuntu:jammy MAINTAINER Heather Ward @@ -12,7 +12,8 @@ RUN apt-get -qq update \ && apt-get -qq install \ wget \ unzip \ - python-dev \ + python2-dev \ + python3-dev \ python3-pip \ zlib1g-dev \ libncurses5-dev \ @@ -24,6 +25,7 @@ RUN apt-get -qq update \ git \ cmake \ && rm -rf /var/lib/apt/lists/* +RUN update-alternatives --install /usr/bin/python python /usr/bin/python2 2 # Need bash for curly brace pattern replace for boost version SHELL ["/bin/bash", "-c"] @@ -76,11 +78,8 @@ ARG PBBAM_VERSION RUN wget https://github.com/PacificBiosciences/pbbam/archive/refs/tags/v${PBBAM_VERSION}.tar.gz \ && tar -zxvf v${PBBAM_VERSION}.tar.gz --directory /opt \ && rm v${PBBAM_VERSION}.tar.gz -# Workaround for "error: ‘ssize’ is not a member of ‘std’; did you mean ‘size’?" RUN cd /opt/pbbam-2.1.0 \ - && sed -i 's~std::ssize~std::size~g' src/PbiFilterTypes.cpp \ && meson build . \ - && cd build \ - && meson install + && meson install -C build ENV LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib/x86_64-linux-gnu/ From 39edfcd58d5edd0d73fd0525dce9f3a5d7357799 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Thu, 15 Jun 2023 12:51:31 -0400 Subject: [PATCH 09/13] Upgrade isoseq to v4.0.0 --- docker/{isoseq3 => isoseq}/Dockerfile | 8 ++++---- docker/isoseq/build.env | 6 ++++++ docker/isoseq3/build.env | 6 ------ 3 files changed, 10 insertions(+), 10 deletions(-) rename docker/{isoseq3 => isoseq}/Dockerfile (64%) create mode 100644 docker/isoseq/build.env delete mode 100644 docker/isoseq3/build.env diff --git a/docker/isoseq3/Dockerfile b/docker/isoseq/Dockerfile similarity index 64% rename from docker/isoseq3/Dockerfile rename to docker/isoseq/Dockerfile index 9c22f59..1b599cd 100644 --- a/docker/isoseq3/Dockerfile +++ b/docker/isoseq/Dockerfile @@ -12,7 +12,7 @@ RUN apt-get -qq update \ wget \ && rm -rf /var/lib/apt/lists/* -ARG ISOSEQ3_VERSION -RUN wget https://github.com/PacificBiosciences/IsoSeq/releases/download/v${ISOSEQ3_VERSION}/isoseq3 --directory-prefix /opt/isoseq3 \ - && chmod +x /opt/isoseq3/isoseq3 \ - && ln -s /opt/isoseq3/isoseq3 /usr/local/bin +ARG ISOSEQ_VERSION +RUN wget https://github.com/PacificBiosciences/IsoSeq/releases/download/v${ISOSEQ_VERSION}/isoseq --directory-prefix /opt/isoseq \ + && chmod +x /opt/isoseq/isoseq \ + && ln -s /opt/isoseq/isoseq /usr/local/bin diff --git a/docker/isoseq/build.env b/docker/isoseq/build.env new file mode 100644 index 0000000..130e8dc --- /dev/null +++ b/docker/isoseq/build.env @@ -0,0 +1,6 @@ +# Tool versions +ISOSEQ_VERSION=4.0.0 + +# Image info +IMAGE_NAME=isoseq +IMAGE_TAG=${ISOSEQ_VERSION} diff --git a/docker/isoseq3/build.env b/docker/isoseq3/build.env deleted file mode 100644 index d00ca9e..0000000 --- a/docker/isoseq3/build.env +++ /dev/null @@ -1,6 +0,0 @@ -# Tool versions -ISOSEQ3_VERSION=3.8.2 - -# Image info -IMAGE_NAME=isoseq3 -IMAGE_TAG=${ISOSEQ3_VERSION} From ef925deed307834a036e32e810ed71de17434a51 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Thu, 15 Jun 2023 14:45:38 -0400 Subject: [PATCH 10/13] Upgrade to version 2.3.0 of pbbam Handles Revio data --- docker/pbbam/Dockerfile | 2 +- docker/pbbam/build.env | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/pbbam/Dockerfile b/docker/pbbam/Dockerfile index eaca09b..e9bb508 100644 --- a/docker/pbbam/Dockerfile +++ b/docker/pbbam/Dockerfile @@ -78,7 +78,7 @@ ARG PBBAM_VERSION RUN wget https://github.com/PacificBiosciences/pbbam/archive/refs/tags/v${PBBAM_VERSION}.tar.gz \ && tar -zxvf v${PBBAM_VERSION}.tar.gz --directory /opt \ && rm v${PBBAM_VERSION}.tar.gz -RUN cd /opt/pbbam-2.1.0 \ +RUN cd /opt/pbbam-${PBBAM_VERSION} \ && meson build . \ && meson install -C build diff --git a/docker/pbbam/build.env b/docker/pbbam/build.env index cc154ff..b6e2157 100644 --- a/docker/pbbam/build.env +++ b/docker/pbbam/build.env @@ -1,11 +1,11 @@ # Tool versions -PBBAM_VERSION=2.1.0 +PBBAM_VERSION=2.3.0 BOOST_VERSION=1.82.0 MESON_VERSION=0.57.0 HTSLIB_VERSION=1.17 SAMTOOLS_VERSION=1.17 NINJA_VERSION=1.11.1 -PBCOPPER_VERSION=2.0.0 +PBCOPPER_VERSION=2.2.0 # Image info IMAGE_NAME=pbbam From e5d640f0b9d8c1024dd711deba6793cfb162073f Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Fri, 16 Jun 2023 12:01:13 -0400 Subject: [PATCH 11/13] Explicitly grant executable to lima binaries to non-root users Singularity runs as non-root --- docker/lima/isoseq/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docker/lima/isoseq/Dockerfile b/docker/lima/isoseq/Dockerfile index 79cf1ad..c1d9695 100644 --- a/docker/lima/isoseq/Dockerfile +++ b/docker/lima/isoseq/Dockerfile @@ -12,10 +12,12 @@ RUN apt-get -qq update \ wget \ && rm -rf /var/lib/apt/lists/* +# Need to explicitly grant executable to non-root users ARG LIMA_VERSION RUN wget https://github.com/PacificBiosciences/barcoding/releases/download/v${LIMA_VERSION}/lima.tar.gz \ && mkdir /opt/lima \ && tar -zxvf lima.tar.gz --directory /opt/lima \ - && rm lima.tar.gz + && rm lima.tar.gz \ + && chmod +x /opt/lima/* ENV PATH ${PATH}:/opt/lima From dab6f6c680bdae82744e411117c5903fa0f10e77 Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Wed, 28 Jun 2023 14:39:17 -0400 Subject: [PATCH 12/13] Update to skera version 1.1.0 --- docker/skera/build.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/skera/build.env b/docker/skera/build.env index cd5f12b..f85ab30 100644 --- a/docker/skera/build.env +++ b/docker/skera/build.env @@ -1,5 +1,5 @@ # Tool versions -SKERA_VERSION=0.1.0 +SKERA_VERSION=1.1.0 # Image info IMAGE_NAME=skera From 8716b22e9e1054c3abbaf6f498427b08f63df18f Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Mon, 24 Jul 2023 15:29:55 -0400 Subject: [PATCH 13/13] Upgrade pigeon to v1.1.0 --- docker/pigeon/Dockerfile | 2 +- docker/pigeon/build.env | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/pigeon/Dockerfile b/docker/pigeon/Dockerfile index 9aa0d77..dcf80ad 100644 --- a/docker/pigeon/Dockerfile +++ b/docker/pigeon/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:focal +FROM ubuntu:jammy MAINTAINER Heather Ward diff --git a/docker/pigeon/build.env b/docker/pigeon/build.env index 993773a..9a5d809 100644 --- a/docker/pigeon/build.env +++ b/docker/pigeon/build.env @@ -1,5 +1,5 @@ # Tool versions -PIGEON_VERSION=1.0.0 +PIGEON_VERSION=1.1.0 # Image info IMAGE_NAME=pigeon