⬆️ Upgrade ICA-AROMA 0.4.3-beta → 0.4.4-beta

Author: shnizzedy

.github/Dockerfiles/ICA-AROMA.0.4.4-beta-bionic.Dockerfile

@@ -0,0 +1,26 @@
+FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS ICA-AROMA
+USER root
+
+# install ICA-AROMA
+RUN mkdir -p /opt/ICA-AROMA
+RUN curl -sL https://github.com/rhr-pruim/ICA-AROMA/archive/v0.4.4-beta.tar.gz | tar -xzC /opt/ICA-AROMA --strip-components 1
+RUN chmod +x /opt/ICA-AROMA/ICA_AROMA.py
+ENV PATH=/opt/ICA-AROMA:$PATH
+
+ENTRYPOINT ["/bin/bash"]
+
+# Link libraries for Singularity images
+RUN ldconfig
+
+RUN apt-get clean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# set user
+USER c-pac_user
+
+# Only keep what we need
+FROM scratch
+LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+ICA-AROMA 0.4.4-beta stage"
+COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/

.github/Dockerfiles/base-lite.Dockerfile

@@ -18,7 +18,7 @@ FROM ghcr.io/fcp-indi/c-pac/afni:23.0.07-bionic as AFNI
 FROM ghcr.io/fcp-indi/c-pac/ants:2.4.3.python3.10-bionic as ANTs
 FROM ghcr.io/fcp-indi/c-pac/connectome-workbench:1.5.0.neurodebian-bionic as connectome-workbench
 FROM ghcr.io/fcp-indi/c-pac/fsl:6.0.6.4-python3.10-bionic as FSL
-FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.3-beta-bionic as ICA-AROMA
+FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.4-beta-bionic as ICA-AROMA
 FROM ghcr.io/fcp-indi/c-pac/msm:2.0-bionic as MSM
 
 FROM ghcr.io/fcp-indi/c-pac/ubuntu:python3.10-bionic-non-free

.github/stage_requirements/ABCD-HCP.txt

@@ -1,9 +1,9 @@
-base-ABCD-HCP.Dockerfile
-AFNI.21.1.00-bionic.Dockerfile
-ANTs.2.2.0.neurodocker-bionic.Dockerfile
-c3d.1.0.0-bionic.Dockerfile
-connectome-workbench.1.3.2-1.neurodebian-bionic.Dockerfile
-FSL.5.0.10-bionic.Dockerfile
-ICA-AROMA.0.4.3-beta-bionic.Dockerfile
-msm.2.0-bionic.Dockerfile
-Ubuntu.bionic-non-free.Dockerfile
+base-ABCD-HCP
+AFNI.21.1.00-bionic
+ANTs.2.2.0.neurodocker-bionic
+c3d.1.0.0-bionic
+connectome-workbench.1.3.2-1.neurodebian-bionic
+FSL.5.0.10-bionic
+ICA-AROMA.0.4.3-beta-bionic
+msm.2.0-bionic
+Ubuntu.bionic-non-free

.github/stage_requirements/fMRIPrep-LTS.txt

@@ -1,9 +1,9 @@
-base-fMRIPrep-LTS.Dockerfile
-AFNI.16.2.07.neurodocker-xenial.Dockerfile
-ANTs.2.3.4.neurodocker-xenial.Dockerfile
-c3d.1.0.0-xenial.Dockerfile
-connectome-workbench.1.3.2-2.neurodebian-xenial.Dockerfile
-FSL.5.0.9-5.neurodebian-xenial.Dockerfile
-ICA-AROMA.0.4.5-xenial.Dockerfile
-msm.2.0-bionic.Dockerfile
-Ubuntu.xenial-20200114.Dockerfile
+base-fMRIPrep-LTS
+AFNI.16.2.07.neurodocker-xenial
+ANTs.2.3.4.neurodocker-xenial
+c3d.1.0.0-xenial
+connectome-workbench.1.3.2-2.neurodebian-xenial
+FSL.5.0.9-5.neurodebian-xenial
+ICA-AROMA.0.4.5-xenial
+msm.2.0-bionic
+Ubuntu.xenial-20200114

.github/stage_requirements/lite.txt

@@ -1,5 +1,5 @@
-base-lite.Dockerfile
-AFNI.21.1.00-bionic.Dockerfile
-ica-aroma.0.4.3-beta-bionic
-msm.2.0-bionic.Dockerfile
-Ubuntu.bionic-non-free.Dockerfile
+base-lite
+AFNI.21.1.00-bionic
+ICA-AROMA.0.4.4-beta-bionic
+msm.2.0-bionic
+Ubuntu.bionic-non-free

.github/stage_requirements/phase_two.txt

@@ -10,5 +10,7 @@ FreeSurfer.7.3.2-Python3.10-bionic
 FSL.5.0.9-5.neurodebian-xenial
 FSL.5.0.10-bionic
 FSL.6.0.6.4-Python3.10-bionic
+ICA-AROMA.0.4.3-beta-bionic
+ICA-AROMA.0.4.4-beta-bionic
 ICA-AROMA.0.4.5-xenial
 msm.2.0-bionic

.github/stage_requirements/standard.txt

@@ -1,2 +1 @@
 lite
-FreeSurfer.7.3.2-Python3.10-bionic

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `AFNI` 21.1.00 'Domitian' → 23.0.07 'Commodus'
 - `ANTs` 2.3.3 'Leptomyrmex' → 2.4.3 'Emplastus'
 - `FSL` 5.0.10 (5.0.9) → 6.0.6 (6.0.4:ddd0a010c)
+- `ICA-AROMA` 0.4.3-beta → 0.4.4-beta
 - `Python` 3.7.13 → 3.10.10 (holding back from 3.11 for `sdcflows`, `torch`, and `torchvision`)
 - `PyPEER` 1.0@`main` → 1.1@`6965d2b`
 - `Torch` 1.2.0+cu92 → 1.13.1