From c0baa1d7bd2f84b009461e9117881842e1fee870 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 13 Nov 2024 11:27:58 -0500 Subject: [PATCH 1/5] Change pennbbl to pennlinc. --- .circleci/config.yml | 8 ++++---- Dockerfile | 22 +++++++++++----------- Dockerfile_TORTOISE | 2 +- Dockerfile_TORTOISEcuda | 2 +- README.rst | 16 ++++++++-------- setup_build.sh | 2 +- 6 files changed, 26 insertions(+), 26 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1a4d99b..667ee59 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -43,11 +43,11 @@ build: &build --rm=false \ -f ${BUILD_FILE} \ --build-arg TAG_ANTS=${TAG_ANTS} \ - -t pennbbl/${IMG_NAME}:${CIRCLE_TAG} . + -t pennlinc/${IMG_NAME}:${CIRCLE_TAG} . if [[ -n "$DOCKER_PASS" ]]; then docker login -u $DOCKER_USER -p $DOCKER_PASS - docker push pennbbl/${IMG_NAME}:$CIRCLE_TAG + docker push pennlinc/${IMG_NAME}:$CIRCLE_TAG fi jobs: @@ -156,7 +156,7 @@ jobs: source setup_build.sh do_build build_fsl docker login -u $DOCKER_USER -p $DOCKER_PASS - docker push pennbbl/qsiprep_build:$CIRCLE_TAG + docker push pennlinc/qsiprep_build:$CIRCLE_TAG fi build_nofsl: @@ -178,7 +178,7 @@ jobs: source setup_build.sh do_build no_fsl docker login -u $DOCKER_USER -p $DOCKER_PASS - docker push pennbbl/qsiprep_build:${CIRCLE_TAG}-nofsl + docker push pennlinc/qsiprep_build:${CIRCLE_TAG}-nofsl fi deployable: diff --git a/Dockerfile b/Dockerfile index 1d15646..395c257 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,17 +15,17 @@ ARG TAG_SYNB0 ARG FSL_BUILD # COPY can't handle variables, so here we go -FROM pennbbl/qsiprep-fsl:${TAG_FSL} as build_fsl -FROM pennbbl/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer -FROM pennbbl/qsiprep-ants:${TAG_ANTS} as build_ants -FROM pennbbl/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3 -FROM pennbbl/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue -FROM pennbbl/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio -FROM pennbbl/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba -FROM pennbbl/qsiprep-afni:${TAG_AFNI} as build_afni -FROM pennbbl/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise -FROM pennbbl/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda -FROM pennbbl/qsiprep-synb0:${TAG_SYNB0} as build_synb0 +FROM pennlinc/qsiprep-fsl:${TAG_FSL} as build_fsl +FROM pennlinc/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer +FROM pennlinc/qsiprep-ants:${TAG_ANTS} as build_ants +FROM pennlinc/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3 +FROM pennlinc/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue +FROM pennlinc/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio +FROM pennlinc/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba +FROM pennlinc/qsiprep-afni:${TAG_AFNI} as build_afni +FROM pennlinc/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise +FROM pennlinc/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda +FROM pennlinc/qsiprep-synb0:${TAG_SYNB0} as build_synb0 FROM pennlinc/atlaspack:0.1.0 as atlaspack FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu diff --git a/Dockerfile_TORTOISE b/Dockerfile_TORTOISE index 85a2f4e..e245ba7 100644 --- a/Dockerfile_TORTOISE +++ b/Dockerfile_TORTOISE @@ -1,6 +1,6 @@ ARG TAG_ANTS -FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base +FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base FROM base as builder RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub diff --git a/Dockerfile_TORTOISEcuda b/Dockerfile_TORTOISEcuda index 24cba82..0d5abc5 100644 --- a/Dockerfile_TORTOISEcuda +++ b/Dockerfile_TORTOISEcuda @@ -1,6 +1,6 @@ ARG TAG_ANTS -FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base +FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base FROM base as builder RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub diff --git a/README.rst b/README.rst index acd1a92..d0a2da1 100644 --- a/README.rst +++ b/README.rst @@ -1,14 +1,14 @@ .. include:: links.rst -QSIprep: Preprocessing and analysis of q-space images -======================================================= +QSIPrep: Preprocessing and analysis of q-space images +===================================================== -.. image:: https://readthedocs.org/projects/qsiprep/badge/?version=latest - :target: http://qsiprep.readthedocs.io/en/latest/?badge=latest - :alt: Documentation Status +.. image:: https://circleci.com/gh/PennLINC/qsiprep_build/tree/master.svg?style=svg + :target: https://circleci.com/gh/PennLINC/qsiprep_build/tree/master -.. image:: https://circleci.com/gh/PennLINC/qsiprep/tree/master.svg?style=svg - :target: https://circleci.com/gh/PennLINC/qsiprep/tree/master +.. image:: https://img.shields.io/badge/docker-pennlinc/qsiprep_build-brightgreen.svg?logo=docker&style=flat + :target: https://hub.docker.com/r/pennlinc/qsiprep_build/tags/ + :alt: Docker Full documentation at https://qsiprep.readthedocs.io @@ -27,7 +27,7 @@ The main features of this software are from Dipy_, MRTrix_, `DSI Studio`_ and others. 4. A novel motion correction algorithm that works on DSI and random q-space sampling schemes -.. image:: https://github.com/PennBBL/qsiprep/raw/master/docs/_static/workflow_full.png +.. image:: https://github.com/PennLINC/qsiprep/raw/master/docs/_static/workflow_full.png .. _preprocessing_def: diff --git a/setup_build.sh b/setup_build.sh index 90a2484..ad0a093 100644 --- a/setup_build.sh +++ b/setup_build.sh @@ -49,7 +49,7 @@ do_build() { DOCKER_BUILDKIT=1 \ BUILDKIT_PROGRESS=plain \ docker build -t \ - pennbbl/qsiprep_build:${THIS_TAG} \ + pennlinc/qsiprep_build:${THIS_TAG} \ --build-arg TAG_FSL=${TAG_FSL} \ --build-arg TAG_FREESURFER=${TAG_FREESURFER} \ --build-arg TAG_ANTS=${TAG_ANTS} \ From b0171c7867847f8721f7b520e23b7db27494dc9f Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 13 Nov 2024 11:57:43 -0500 Subject: [PATCH 2/5] Use the component images from PennBBL. --- Dockerfile | 24 ++++++++++++------------ Dockerfile_3Tissue | 2 +- Dockerfile_TORTOISE | 2 +- Dockerfile_TORTOISEcuda | 2 +- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/Dockerfile b/Dockerfile index 395c257..0398afe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,18 +15,18 @@ ARG TAG_SYNB0 ARG FSL_BUILD # COPY can't handle variables, so here we go -FROM pennlinc/qsiprep-fsl:${TAG_FSL} as build_fsl -FROM pennlinc/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer -FROM pennlinc/qsiprep-ants:${TAG_ANTS} as build_ants -FROM pennlinc/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3 -FROM pennlinc/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue -FROM pennlinc/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio -FROM pennlinc/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba -FROM pennlinc/qsiprep-afni:${TAG_AFNI} as build_afni -FROM pennlinc/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise -FROM pennlinc/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda -FROM pennlinc/qsiprep-synb0:${TAG_SYNB0} as build_synb0 -FROM pennlinc/atlaspack:0.1.0 as atlaspack +FROM pennbbl/qsiprep-fsl:${TAG_FSL} as build_fsl +FROM pennbbl/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer +FROM pennbbl/qsiprep-ants:${TAG_ANTS} as build_ants +FROM pennbbl/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3 +FROM pennbbl/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue +FROM pennbbl/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio +FROM pennbbl/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba +FROM pennbbl/qsiprep-afni:${TAG_AFNI} as build_afni +FROM pennbbl/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise +FROM pennbbl/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda +FROM pennbbl/qsiprep-synb0:${TAG_SYNB0} as build_synb0 +FROM pennbbl/atlaspack:0.1.0 as atlaspack FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu # Make a dummy fsl image containing no FSL diff --git a/Dockerfile_3Tissue b/Dockerfile_3Tissue index 77c2ca7..6251a1e 100644 --- a/Dockerfile_3Tissue +++ b/Dockerfile_3Tissue @@ -8,7 +8,7 @@ RUN apt-get update && \ ARG MRTRIX_SHA=5f4c31bc93008520c61d59b94af0db3f17b4ab76 ENV PATH="/opt/mrtrix3-latest/bin:$PATH" RUN cd /opt \ -&& curl -sSLO https://github.com/PennLINC/MRtrix3Tissue/archive/${MRTRIX_SHA}.zip \ +&& curl -sSLO https://github.com/pennbbl/MRtrix3Tissue/archive/${MRTRIX_SHA}.zip \ && unzip ${MRTRIX_SHA}.zip \ && mv MRtrix3Tissue-${MRTRIX_SHA} /opt/3Tissue \ && rm ${MRTRIX_SHA}.zip \ diff --git a/Dockerfile_TORTOISE b/Dockerfile_TORTOISE index e245ba7..85a2f4e 100644 --- a/Dockerfile_TORTOISE +++ b/Dockerfile_TORTOISE @@ -1,6 +1,6 @@ ARG TAG_ANTS -FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base +FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base FROM base as builder RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub diff --git a/Dockerfile_TORTOISEcuda b/Dockerfile_TORTOISEcuda index 0d5abc5..24cba82 100644 --- a/Dockerfile_TORTOISEcuda +++ b/Dockerfile_TORTOISEcuda @@ -1,6 +1,6 @@ ARG TAG_ANTS -FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base +FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base FROM base as builder RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub From b06a4929b9d2d41f30d70d9782fa3b21c8c1445a Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 13 Nov 2024 11:58:16 -0500 Subject: [PATCH 3/5] Fix link. --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0398afe..1d15646 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,7 +26,7 @@ FROM pennbbl/qsiprep-afni:${TAG_AFNI} as build_afni FROM pennbbl/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise FROM pennbbl/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda FROM pennbbl/qsiprep-synb0:${TAG_SYNB0} as build_synb0 -FROM pennbbl/atlaspack:0.1.0 as atlaspack +FROM pennlinc/atlaspack:0.1.0 as atlaspack FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu # Make a dummy fsl image containing no FSL From 8c4e098d768a3ba7b967423be5fd09580f421fdf Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 13 Nov 2024 12:00:24 -0500 Subject: [PATCH 4/5] whoops --- Dockerfile_3Tissue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile_3Tissue b/Dockerfile_3Tissue index 6251a1e..77c2ca7 100644 --- a/Dockerfile_3Tissue +++ b/Dockerfile_3Tissue @@ -8,7 +8,7 @@ RUN apt-get update && \ ARG MRTRIX_SHA=5f4c31bc93008520c61d59b94af0db3f17b4ab76 ENV PATH="/opt/mrtrix3-latest/bin:$PATH" RUN cd /opt \ -&& curl -sSLO https://github.com/pennbbl/MRtrix3Tissue/archive/${MRTRIX_SHA}.zip \ +&& curl -sSLO https://github.com/PennLINC/MRtrix3Tissue/archive/${MRTRIX_SHA}.zip \ && unzip ${MRTRIX_SHA}.zip \ && mv MRtrix3Tissue-${MRTRIX_SHA} /opt/3Tissue \ && rm ${MRTRIX_SHA}.zip \ From 65d32ceb5b45ed8c5bb393569e0763460c5137c1 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 13 Nov 2024 12:40:03 -0500 Subject: [PATCH 5/5] Replace all pennbbl with pennlinc. --- Dockerfile | 22 +++++++++++----------- Dockerfile_TORTOISE | 2 +- Dockerfile_TORTOISEcuda | 2 +- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1d15646..395c257 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,17 +15,17 @@ ARG TAG_SYNB0 ARG FSL_BUILD # COPY can't handle variables, so here we go -FROM pennbbl/qsiprep-fsl:${TAG_FSL} as build_fsl -FROM pennbbl/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer -FROM pennbbl/qsiprep-ants:${TAG_ANTS} as build_ants -FROM pennbbl/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3 -FROM pennbbl/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue -FROM pennbbl/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio -FROM pennbbl/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba -FROM pennbbl/qsiprep-afni:${TAG_AFNI} as build_afni -FROM pennbbl/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise -FROM pennbbl/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda -FROM pennbbl/qsiprep-synb0:${TAG_SYNB0} as build_synb0 +FROM pennlinc/qsiprep-fsl:${TAG_FSL} as build_fsl +FROM pennlinc/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer +FROM pennlinc/qsiprep-ants:${TAG_ANTS} as build_ants +FROM pennlinc/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3 +FROM pennlinc/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue +FROM pennlinc/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio +FROM pennlinc/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba +FROM pennlinc/qsiprep-afni:${TAG_AFNI} as build_afni +FROM pennlinc/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise +FROM pennlinc/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda +FROM pennlinc/qsiprep-synb0:${TAG_SYNB0} as build_synb0 FROM pennlinc/atlaspack:0.1.0 as atlaspack FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu diff --git a/Dockerfile_TORTOISE b/Dockerfile_TORTOISE index 85a2f4e..e245ba7 100644 --- a/Dockerfile_TORTOISE +++ b/Dockerfile_TORTOISE @@ -1,6 +1,6 @@ ARG TAG_ANTS -FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base +FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base FROM base as builder RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub diff --git a/Dockerfile_TORTOISEcuda b/Dockerfile_TORTOISEcuda index 24cba82..0d5abc5 100644 --- a/Dockerfile_TORTOISEcuda +++ b/Dockerfile_TORTOISEcuda @@ -1,6 +1,6 @@ ARG TAG_ANTS -FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base +FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base FROM base as builder RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub