diff --git a/.datalad/config b/.datalad/config index 72e40049..83c7497d 100644 --- a/.datalad/config +++ b/.datalad/config @@ -33,7 +33,7 @@ image = images/bids/bids-fibredensityandcrosssection--0.0.1.sing [datalad "containers.bids-fmriprep"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} - image = images/bids/bids-fmriprep--24.0.1.sing + image = images/bids/bids-fmriprep--24.1.1.sing [datalad "containers.bids-freesurfer"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} image = images/bids/bids-freesurfer--7.4.1-unstable.sing @@ -78,7 +78,7 @@ image = images/bids/bids-tracula--6.0.0.beta-0.sing [datalad "containers.bids-validator"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} - image = images/bids/bids-validator--1.14.10.sing + image = images/bids/bids-validator--1.14.14.sing [datalad "containers.neuronets-kwyk"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} image = images/neuronets/neuronets-kwyk--0.5.0-gpu.sing @@ -97,7 +97,7 @@ image = images/repronim/repronim-ptb-3--3.0.15.20190401.dfsg1-1+nd100.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-qsiprep"] - image = images/bids/bids-qsiprep--0.22.1.sing + image = images/bids/bids-qsiprep--0.23.0.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-pymvpa"] image = images/bids/bids-pymvpa--4.0.4.sing @@ -124,7 +124,7 @@ image = images/bids/bids-micapipe--0.0.1.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.nipy-heudiconv"] - image = images/nipy/nipy-heudiconv--1.1.6.sing + image = images/nipy/nipy-heudiconv--1.3.1.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-funcmasker-flex"] image = images/bids/bids-funcmasker-flex--0.2.0.sing @@ -133,7 +133,7 @@ image = images/bids/bids-dmriprep--0.5.0.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-nibabies"] - image = images/bids/bids-nibabies--23.1.0.sing + image = images/bids/bids-nibabies--24.1.0.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-nirodents"] image = images/bids/bids-nirodents--0.2.1.sing @@ -172,7 +172,7 @@ image = images/brainiak/brainiak-rtcloudlite--1.4.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-bidspm"] - image = images/bids/bids-bidspm--3.0.0.sing + image = images/bids/bids-bidspm--4.0.0.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-bidsmreye"] image = images/bids/bids-bidsmreye--0.5.0.sing @@ -196,7 +196,7 @@ image = images/neurodesk/neurodesk-spm12--r7771.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-spinalcordtoolbox"] - image = images/neurodesk/neurodesk-spinalcordtoolbox--5.8.simg + image = images/neurodesk/neurodesk-spinalcordtoolbox--6.4.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-sovabids"] image = images/neurodesk/neurodesk-sovabids--0.3.1a0.simg @@ -223,7 +223,7 @@ image = images/neurodesk/neurodesk-rabies--0.3.5.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-qsmxt"] - image = images/neurodesk/neurodesk-qsmxt--7.1.0.simg + image = images/neurodesk/neurodesk-qsmxt--7.2.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-physio"] image = images/neurodesk/neurodesk-physio--r2021a.simg @@ -298,13 +298,13 @@ image = images/neurodesk/neurodesk-gimp--2.10.18.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fsl"] - image = images/neurodesk/neurodesk-fsl--6.0.7.4.simg + image = images/neurodesk/neurodesk-fsl--6.0.7.14.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-freesurfer"] image = images/neurodesk/neurodesk-freesurfer--7.4.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fmriprep"] - image = images/neurodesk/neurodesk-fmriprep--23.2.1.simg + image = images/neurodesk/neurodesk-fmriprep--24.1.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-fieldtrip"] image = images/neurodesk/neurodesk-fieldtrip--20220617.simg @@ -316,7 +316,7 @@ image = images/neurodesk/neurodesk-eeglab--2020.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-dsistudio"] - image = images/neurodesk/neurodesk-dsistudio--chen.2024.04.19.simg + image = images/neurodesk/neurodesk-dsistudio--2024.06.12.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-diffusiontoolkit"] image = images/neurodesk/neurodesk-diffusiontoolkit--0.6.4.1.simg @@ -352,7 +352,7 @@ image = images/neurodesk/neurodesk-bidstools--1.0.4.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-bidscoin"] - image = images/neurodesk/neurodesk-bidscoin--4.3.3.simg + image = images/neurodesk/neurodesk-bidscoin--4.4.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-bart"] image = images/neurodesk/neurodesk-bart--0.9.00.simg @@ -361,16 +361,16 @@ image = images/neurodesk/neurodesk-ashs--2.0.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-aslprep"] - image = images/neurodesk/neurodesk-aslprep--0.7.0.simg + image = images/neurodesk/neurodesk-aslprep--0.7.2.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-ants"] - image = images/neurodesk/neurodesk-ants--2.5.1.simg + image = images/neurodesk/neurodesk-ants--2.5.3.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-aidamri"] image = images/neurodesk/neurodesk-aidamri--1.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-afni"] - image = images/neurodesk/neurodesk-afni--24.1.02.simg + image = images/neurodesk/neurodesk-afni--24.3.00.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mfcsc"] image = images/neurodesk/neurodesk-mfcsc--1.1.simg @@ -424,10 +424,10 @@ image = images/neurodesk/neurodesk-hmri--0.6.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-xcp-d"] - image = images/bids/bids-xcp-d--0.8.3.sing + image = images/bids/bids-xcp-d--0.9.1.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-aslprep"] - image = images/bids/bids-aslprep--0.7.2.sing + image = images/bids/bids-aslprep--0.7.3.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-vesselboost"] image = images/neurodesk/neurodesk-vesselboost--1.0.0.simg @@ -469,10 +469,10 @@ image = images/neurodesk/neurodesk-nighres--1.5.1.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-bibsnet"] - image = images/bids/bids-bibsnet--3.4.1.sing + image = images/bids/bids-bibsnet--3.4.2.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-petdeface"] - image = images/bids/bids-petdeface--0.1.1.sing + image = images/bids/bids-petdeface--0.2.1.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mrtrix3src"] image = images/neurodesk/neurodesk-mrtrix3src--latest.simg @@ -483,3 +483,27 @@ [datalad "containers.neurodesk-qmrlab"] image = images/neurodesk/neurodesk-qmrlab--2.4.2.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.neurodesk-niimath"] + image = images/neurodesk/neurodesk-niimath--1.0.0.simg + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.bids-qsirecon"] + image = images/bids/bids-qsirecon--0.23.2.sing + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.bids-reproa"] + image = images/bids/bids-reproa--0.2.1.sing + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.neurodesk-micapipe"] + image = images/neurodesk/neurodesk-micapipe--v0.2.3.simg + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.neurodesk-dcm2niix"] + image = images/neurodesk/neurodesk-dcm2niix--v1.0.20240202.simg + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.neurodesk-brainnetviewer"] + image = images/neurodesk/neurodesk-brainnetviewer--1.7.20191031.simg + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.neurodesk-brainlifecli"] + image = images/neurodesk/neurodesk-brainlifecli--1.7.0.simg + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} +[datalad "containers.neurodesk-vmtk"] + image = images/neurodesk/neurodesk-vmtk--1.5.0.simg + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} diff --git a/README.md b/README.md index 28c700ab..a801e850 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # ReproNim/containers - containerized environments for reproducible neuroimaging -[![CI Status](https://github.com/RepoNim/containers/actions/workflows/base-tests.yaml/badge.svg)](https://github.com/RepoNim/containers/actions/workflows/base-tests.yaml) +[![CI Status](https://github.com/ReproNim/containers/actions/workflows/base-tests.yaml/badge.svg)](https://github.com/ReproNim/containers/actions/workflows/base-tests.yaml) [![Additional tests](https://github.com/ReproNim/containers/workflows/Additional%20tests/badge.svg)](https://github.com/ReproNim/containers/actions?query=workflow%3A%22Additional+tests%22) This repository provides a [DataLad] dataset (git/git-annex diff --git a/images/bids/Singularity.bids-aslprep--0.7.3 b/images/bids/Singularity.bids-aslprep--0.7.3 new file mode 100644 index 00000000..e46dc47c --- /dev/null +++ b/images/bids/Singularity.bids-aslprep--0.7.3 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennlinc/aslprep:0.7.3 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-bibsnet--3.4.2 b/images/bids/Singularity.bids-bibsnet--3.4.2 new file mode 100644 index 00000000..074df58e --- /dev/null +++ b/images/bids/Singularity.bids-bibsnet--3.4.2 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: dcanumn/bibsnet:release-3.4.2 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-bidspm--4.0.0 b/images/bids/Singularity.bids-bidspm--4.0.0 new file mode 100644 index 00000000..962d13ca --- /dev/null +++ b/images/bids/Singularity.bids-bidspm--4.0.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: cpplab/bidspm:4.0.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-fmriprep--24.1.0 b/images/bids/Singularity.bids-fmriprep--24.1.0 new file mode 100644 index 00000000..e0e225fb --- /dev/null +++ b/images/bids/Singularity.bids-fmriprep--24.1.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipreps/fmriprep:24.1.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-fmriprep--24.1.1 b/images/bids/Singularity.bids-fmriprep--24.1.1 new file mode 100644 index 00000000..1d4dac3f --- /dev/null +++ b/images/bids/Singularity.bids-fmriprep--24.1.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipreps/fmriprep:24.1.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-mriqc--24.0.2 b/images/bids/Singularity.bids-mriqc--24.0.2 index cb7ee748..080cd57e 100644 --- a/images/bids/Singularity.bids-mriqc--24.0.2 +++ b/images/bids/Singularity.bids-mriqc--24.0.2 @@ -6,6 +6,10 @@ Bootstrap: docker From: nipreps/mriqc:24.0.2 %post +# Bugfix +# https://github.com/nipreps/mriqc/issues/1304 +chmod a+rX -R /opt + # Create commonly present root directories to avoid need in overlays not supported # on older systems diff --git a/images/bids/Singularity.bids-nibabies--24.0.1 b/images/bids/Singularity.bids-nibabies--24.0.1 new file mode 100644 index 00000000..8fe4006a --- /dev/null +++ b/images/bids/Singularity.bids-nibabies--24.0.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipreps/nibabies:24.0.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-nibabies--24.1.0 b/images/bids/Singularity.bids-nibabies--24.1.0 new file mode 100644 index 00000000..1b5fbe4f --- /dev/null +++ b/images/bids/Singularity.bids-nibabies--24.1.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipreps/nibabies:24.1.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-petdeface--0.2.1 b/images/bids/Singularity.bids-petdeface--0.2.1 new file mode 100644 index 00000000..a8dee040 --- /dev/null +++ b/images/bids/Singularity.bids-petdeface--0.2.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: openneuropet/petdeface:0.2.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-qsiprep--0.23.0 b/images/bids/Singularity.bids-qsiprep--0.23.0 new file mode 100644 index 00000000..ec300512 --- /dev/null +++ b/images/bids/Singularity.bids-qsiprep--0.23.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennbbl/qsiprep:0.23.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-qsirecon--0.23.1 b/images/bids/Singularity.bids-qsirecon--0.23.1 new file mode 100644 index 00000000..b532c9f0 --- /dev/null +++ b/images/bids/Singularity.bids-qsirecon--0.23.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennlinc/qsirecon:0.23.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-qsirecon--0.23.2 b/images/bids/Singularity.bids-qsirecon--0.23.2 new file mode 100644 index 00000000..ceb08d39 --- /dev/null +++ b/images/bids/Singularity.bids-qsirecon--0.23.2 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennlinc/qsirecon:0.23.2 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-qsirecon--unstable b/images/bids/Singularity.bids-qsirecon--unstable new file mode 100644 index 00000000..c0b3ffb3 --- /dev/null +++ b/images/bids/Singularity.bids-qsirecon--unstable @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennlinc/qsirecon:unstable + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-reproa--0.2.1 b/images/bids/Singularity.bids-reproa--0.2.1 new file mode 100644 index 00000000..7a2f578f --- /dev/null +++ b/images/bids/Singularity.bids-reproa--0.2.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: reprostat/reproa:0.2.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-validator--1.14.11 b/images/bids/Singularity.bids-validator--1.14.11 new file mode 100644 index 00000000..3a8b35fc --- /dev/null +++ b/images/bids/Singularity.bids-validator--1.14.11 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: bids/validator:v1.14.11 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-validator--1.14.12 b/images/bids/Singularity.bids-validator--1.14.12 new file mode 100644 index 00000000..4ad75401 --- /dev/null +++ b/images/bids/Singularity.bids-validator--1.14.12 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: bids/validator:v1.14.12 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-validator--1.14.13 b/images/bids/Singularity.bids-validator--1.14.13 new file mode 100644 index 00000000..f2dbd076 --- /dev/null +++ b/images/bids/Singularity.bids-validator--1.14.13 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: bids/validator:v1.14.13 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-validator--1.14.14 b/images/bids/Singularity.bids-validator--1.14.14 new file mode 100644 index 00000000..412bbb38 --- /dev/null +++ b/images/bids/Singularity.bids-validator--1.14.14 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: bids/validator:v1.14.14 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-xcp-d--0.9.0 b/images/bids/Singularity.bids-xcp-d--0.9.0 new file mode 100644 index 00000000..2d699b26 --- /dev/null +++ b/images/bids/Singularity.bids-xcp-d--0.9.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennlinc/xcp_d:0.9.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/Singularity.bids-xcp-d--0.9.1 b/images/bids/Singularity.bids-xcp-d--0.9.1 new file mode 100644 index 00000000..b957ce0a --- /dev/null +++ b/images/bids/Singularity.bids-xcp-d--0.9.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: pennlinc/xcp_d:0.9.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/bids/bids-aslprep--0.7.3.sing b/images/bids/bids-aslprep--0.7.3.sing new file mode 120000 index 00000000..e71b0ae8 --- /dev/null +++ b/images/bids/bids-aslprep--0.7.3.sing @@ -0,0 +1 @@ +../../.git/annex/objects/jQ/8m/MD5E-s3049938975--9f601f7f5198d70a39797a34ef9c0ebe.3.sing/MD5E-s3049938975--9f601f7f5198d70a39797a34ef9c0ebe.3.sing \ No newline at end of file diff --git a/images/bids/bids-bibsnet--3.4.2.sing b/images/bids/bids-bibsnet--3.4.2.sing new file mode 120000 index 00000000..4aaf9e86 --- /dev/null +++ b/images/bids/bids-bibsnet--3.4.2.sing @@ -0,0 +1 @@ +../../.git/annex/objects/W9/mg/MD5E-s13121511455--13cd922ec5f841b9685879df1841de74.2.sing/MD5E-s13121511455--13cd922ec5f841b9685879df1841de74.2.sing \ No newline at end of file diff --git a/images/bids/bids-bidspm--4.0.0.sing b/images/bids/bids-bidspm--4.0.0.sing new file mode 120000 index 00000000..40e4e803 --- /dev/null +++ b/images/bids/bids-bidspm--4.0.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/JQ/G5/MD5E-s837378079--032bb3c93302bc1719d15247db3abdd5.0.sing/MD5E-s837378079--032bb3c93302bc1719d15247db3abdd5.0.sing \ No newline at end of file diff --git a/images/bids/bids-fmriprep--24.1.0.sing b/images/bids/bids-fmriprep--24.1.0.sing new file mode 120000 index 00000000..6b2f780b --- /dev/null +++ b/images/bids/bids-fmriprep--24.1.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/1G/F8/MD5E-s2737958943--b460d380225dc83a71b43cb36b4e47d1.0.sing/MD5E-s2737958943--b460d380225dc83a71b43cb36b4e47d1.0.sing \ No newline at end of file diff --git a/images/bids/bids-fmriprep--24.1.1.sing b/images/bids/bids-fmriprep--24.1.1.sing new file mode 120000 index 00000000..26330424 --- /dev/null +++ b/images/bids/bids-fmriprep--24.1.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/gz/6k/MD5E-s2666061855--65f2a2c31e81905568c55eb999f3f0b9.1.sing/MD5E-s2666061855--65f2a2c31e81905568c55eb999f3f0b9.1.sing \ No newline at end of file diff --git a/images/bids/bids-mriqc--24.0.2.sing b/images/bids/bids-mriqc--24.0.2.sing index 9b125150..6e7ee269 120000 --- a/images/bids/bids-mriqc--24.0.2.sing +++ b/images/bids/bids-mriqc--24.0.2.sing @@ -1 +1 @@ -../../.git/annex/objects/G4/MM/MD5E-s4953477151--63f716ef8a392183b13366e9c9c97fb3.2.sing/MD5E-s4953477151--63f716ef8a392183b13366e9c9c97fb3.2.sing \ No newline at end of file +../../.git/annex/objects/q6/Xw/MD5E-s4953473055--338868dedf9eaf6a00450e2ab16efa73.2.sing/MD5E-s4953473055--338868dedf9eaf6a00450e2ab16efa73.2.sing \ No newline at end of file diff --git a/images/bids/bids-nibabies--24.0.1.sing b/images/bids/bids-nibabies--24.0.1.sing new file mode 120000 index 00000000..cf8f8f4b --- /dev/null +++ b/images/bids/bids-nibabies--24.0.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/6K/6k/MD5E-s4227158047--2be6f358b88b5aa140c1fa325511f4d6.1.sing/MD5E-s4227158047--2be6f358b88b5aa140c1fa325511f4d6.1.sing \ No newline at end of file diff --git a/images/bids/bids-nibabies--24.1.0.sing b/images/bids/bids-nibabies--24.1.0.sing new file mode 120000 index 00000000..4ec9c14c --- /dev/null +++ b/images/bids/bids-nibabies--24.1.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/W3/Jq/MD5E-s4159365151--21c6e76c743b445a40689334572c274d.0.sing/MD5E-s4159365151--21c6e76c743b445a40689334572c274d.0.sing \ No newline at end of file diff --git a/images/bids/bids-petdeface--0.2.1.sing b/images/bids/bids-petdeface--0.2.1.sing new file mode 120000 index 00000000..b1f85965 --- /dev/null +++ b/images/bids/bids-petdeface--0.2.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/Fz/wq/MD5E-s10145787935--016bad2b9bf028e7ab0d0b2bf4c4f354.1.sing/MD5E-s10145787935--016bad2b9bf028e7ab0d0b2bf4c4f354.1.sing \ No newline at end of file diff --git a/images/bids/bids-qsiprep--0.23.0.sing b/images/bids/bids-qsiprep--0.23.0.sing new file mode 120000 index 00000000..6abd8089 --- /dev/null +++ b/images/bids/bids-qsiprep--0.23.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/6V/Gj/MD5E-s7835189279--22d49602b8d02bad6315d38df3947eff.0.sing/MD5E-s7835189279--22d49602b8d02bad6315d38df3947eff.0.sing \ No newline at end of file diff --git a/images/bids/bids-qsirecon--0.23.1.sing b/images/bids/bids-qsirecon--0.23.1.sing new file mode 120000 index 00000000..0ac8d3ba --- /dev/null +++ b/images/bids/bids-qsirecon--0.23.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/pM/WQ/MD5E-s7024902175--be1a8f8df514f5a63ed3dc9b438b241e.1.sing/MD5E-s7024902175--be1a8f8df514f5a63ed3dc9b438b241e.1.sing \ No newline at end of file diff --git a/images/bids/bids-qsirecon--0.23.2.sing b/images/bids/bids-qsirecon--0.23.2.sing new file mode 120000 index 00000000..0a3c60eb --- /dev/null +++ b/images/bids/bids-qsirecon--0.23.2.sing @@ -0,0 +1 @@ +../../.git/annex/objects/v3/Fk/MD5E-s7024939039--4f7638bee6dd1e54854da8d4c19782f5.2.sing/MD5E-s7024939039--4f7638bee6dd1e54854da8d4c19782f5.2.sing \ No newline at end of file diff --git a/images/bids/bids-qsirecon--unstable.sing b/images/bids/bids-qsirecon--unstable.sing new file mode 120000 index 00000000..e58b987f --- /dev/null +++ b/images/bids/bids-qsirecon--unstable.sing @@ -0,0 +1 @@ +../../.git/annex/objects/g0/Q3/MD5E-s7053414431--e0615fbf3295ec495c24afcd08b17b8a.sing/MD5E-s7053414431--e0615fbf3295ec495c24afcd08b17b8a.sing \ No newline at end of file diff --git a/images/bids/bids-reproa--0.2.1.sing b/images/bids/bids-reproa--0.2.1.sing new file mode 120000 index 00000000..079bf165 --- /dev/null +++ b/images/bids/bids-reproa--0.2.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/Q4/Gx/MD5E-s2204295199--e376a78af26b47a7e1ce57f72c35aac5.1.sing/MD5E-s2204295199--e376a78af26b47a7e1ce57f72c35aac5.1.sing \ No newline at end of file diff --git a/images/bids/bids-validator--1.14.11.sing b/images/bids/bids-validator--1.14.11.sing new file mode 120000 index 00000000..1c2b3663 --- /dev/null +++ b/images/bids/bids-validator--1.14.11.sing @@ -0,0 +1 @@ +../../.git/annex/objects/2v/X8/MD5E-s334143519--4f5d852d7ecc11eadcb03cd89db2512e.11.sing/MD5E-s334143519--4f5d852d7ecc11eadcb03cd89db2512e.11.sing \ No newline at end of file diff --git a/images/bids/bids-validator--1.14.12.sing b/images/bids/bids-validator--1.14.12.sing new file mode 120000 index 00000000..f7e2529b --- /dev/null +++ b/images/bids/bids-validator--1.14.12.sing @@ -0,0 +1 @@ +../../.git/annex/objects/gm/ZG/MD5E-s334151711--fec3ae81f6a760dfef444daee22eb997.12.sing/MD5E-s334151711--fec3ae81f6a760dfef444daee22eb997.12.sing \ No newline at end of file diff --git a/images/bids/bids-validator--1.14.13.sing b/images/bids/bids-validator--1.14.13.sing new file mode 120000 index 00000000..6d4f4b37 --- /dev/null +++ b/images/bids/bids-validator--1.14.13.sing @@ -0,0 +1 @@ +../../.git/annex/objects/w5/mp/MD5E-s337874975--ac8d343f2c6d95a78b6c4f34a1042deb.13.sing/MD5E-s337874975--ac8d343f2c6d95a78b6c4f34a1042deb.13.sing \ No newline at end of file diff --git a/images/bids/bids-validator--1.14.14.sing b/images/bids/bids-validator--1.14.14.sing new file mode 120000 index 00000000..d922f86e --- /dev/null +++ b/images/bids/bids-validator--1.14.14.sing @@ -0,0 +1 @@ +../../.git/annex/objects/vp/G7/MD5E-s349659167--608ab2b5323a249fb4f14fbc4086f82a.14.sing/MD5E-s349659167--608ab2b5323a249fb4f14fbc4086f82a.14.sing \ No newline at end of file diff --git a/images/bids/bids-xcp-d--0.9.0.sing b/images/bids/bids-xcp-d--0.9.0.sing new file mode 120000 index 00000000..271ab16d --- /dev/null +++ b/images/bids/bids-xcp-d--0.9.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/8Z/XP/MD5E-s5591523359--a5bacd6e74e94476b62709f895d5d6bf.0.sing/MD5E-s5591523359--a5bacd6e74e94476b62709f895d5d6bf.0.sing \ No newline at end of file diff --git a/images/bids/bids-xcp-d--0.9.1.sing b/images/bids/bids-xcp-d--0.9.1.sing new file mode 120000 index 00000000..d424e7a4 --- /dev/null +++ b/images/bids/bids-xcp-d--0.9.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/Jm/vj/MD5E-s5515673631--c28b2c52389f1be334c6044910f92164.1.sing/MD5E-s5515673631--c28b2c52389f1be334c6044910f92164.1.sing \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--24.2.07.simg b/images/neurodesk/neurodesk-afni--24.2.07.simg new file mode 120000 index 00000000..f413efda --- /dev/null +++ b/images/neurodesk/neurodesk-afni--24.2.07.simg @@ -0,0 +1 @@ +../../.git/annex/objects/2Q/Mk/MD5E-s8703946752--e5b36adf173e6756f7037354c73a51ea.07.simg/MD5E-s8703946752--e5b36adf173e6756f7037354c73a51ea.07.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-afni--24.3.00.simg b/images/neurodesk/neurodesk-afni--24.3.00.simg new file mode 120000 index 00000000..54e82157 --- /dev/null +++ b/images/neurodesk/neurodesk-afni--24.3.00.simg @@ -0,0 +1 @@ +../../.git/annex/objects/vg/x2/MD5E-s8703823872--ab4bfe1141383df34cea6e3fb4b3e409.00.simg/MD5E-s8703823872--ab4bfe1141383df34cea6e3fb4b3e409.00.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-ants--2.5.3.simg b/images/neurodesk/neurodesk-ants--2.5.3.simg new file mode 120000 index 00000000..4579f360 --- /dev/null +++ b/images/neurodesk/neurodesk-ants--2.5.3.simg @@ -0,0 +1 @@ +../../.git/annex/objects/18/qf/MD5E-s246034432--8bbca3fff3de728b65940e571bff93b9.3.simg/MD5E-s246034432--8bbca3fff3de728b65940e571bff93b9.3.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-aslprep--0.7.2.simg b/images/neurodesk/neurodesk-aslprep--0.7.2.simg new file mode 120000 index 00000000..fe5c9abf --- /dev/null +++ b/images/neurodesk/neurodesk-aslprep--0.7.2.simg @@ -0,0 +1 @@ +../../.git/annex/objects/2F/g9/MD5E-s3055484928--98797e7dee4e0c5c3a55d4eca16762b4.2.simg/MD5E-s3055484928--98797e7dee4e0c5c3a55d4eca16762b4.2.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-bidscoin--4.4.0.simg b/images/neurodesk/neurodesk-bidscoin--4.4.0.simg new file mode 120000 index 00000000..cb442494 --- /dev/null +++ b/images/neurodesk/neurodesk-bidscoin--4.4.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/jq/GZ/MD5E-s892665856--ad19659bcb832f10d66e091aabba3880.0.simg/MD5E-s892665856--ad19659bcb832f10d66e091aabba3880.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-brainlifecli--1.7.0.simg b/images/neurodesk/neurodesk-brainlifecli--1.7.0.simg new file mode 120000 index 00000000..47ccf6a2 --- /dev/null +++ b/images/neurodesk/neurodesk-brainlifecli--1.7.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Gw/0K/MD5E-s525918208--63944e8405da6b2f21a74509e69cc5e0.0.simg/MD5E-s525918208--63944e8405da6b2f21a74509e69cc5e0.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-brainnetviewer--1.7.20191031.simg b/images/neurodesk/neurodesk-brainnetviewer--1.7.20191031.simg new file mode 120000 index 00000000..aa129fb9 --- /dev/null +++ b/images/neurodesk/neurodesk-brainnetviewer--1.7.20191031.simg @@ -0,0 +1 @@ +../../.git/annex/objects/9g/GF/MD5E-s2250715136--a91df5efb49b11e8fbc0e6c3e4131833.simg/MD5E-s2250715136--a91df5efb49b11e8fbc0e6c3e4131833.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-dcm2niix--v1.0.20240202.simg b/images/neurodesk/neurodesk-dcm2niix--v1.0.20240202.simg new file mode 120000 index 00000000..4bc0a8ce --- /dev/null +++ b/images/neurodesk/neurodesk-dcm2niix--v1.0.20240202.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Pq/VG/MD5E-s65720320--b0e698c151f1cbbd9683bdf30cc67002.simg/MD5E-s65720320--b0e698c151f1cbbd9683bdf30cc67002.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-dsistudio--2024.06.12.simg b/images/neurodesk/neurodesk-dsistudio--2024.06.12.simg new file mode 120000 index 00000000..e4ae9483 --- /dev/null +++ b/images/neurodesk/neurodesk-dsistudio--2024.06.12.simg @@ -0,0 +1 @@ +../../.git/annex/objects/WW/FV/MD5E-s367882240--87764a258c2147db8d7bd2605fe17439.12.simg/MD5E-s367882240--87764a258c2147db8d7bd2605fe17439.12.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-fmriprep--24.1.0.simg b/images/neurodesk/neurodesk-fmriprep--24.1.0.simg new file mode 120000 index 00000000..811e83dd --- /dev/null +++ b/images/neurodesk/neurodesk-fmriprep--24.1.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/vv/2f/MD5E-s2743914496--192e47b52f9ca87f96582aa15dde4be7.0.simg/MD5E-s2743914496--192e47b52f9ca87f96582aa15dde4be7.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-fsl--6.0.7.14.simg b/images/neurodesk/neurodesk-fsl--6.0.7.14.simg new file mode 120000 index 00000000..7647f7f9 --- /dev/null +++ b/images/neurodesk/neurodesk-fsl--6.0.7.14.simg @@ -0,0 +1 @@ +../../.git/annex/objects/qG/8X/MD5E-s6078599168--ea09b5975df3309dca24c6f9f50dba42.14.simg/MD5E-s6078599168--ea09b5975df3309dca24c6f9f50dba42.14.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-fsl--6.0.7.8.simg b/images/neurodesk/neurodesk-fsl--6.0.7.8.simg new file mode 120000 index 00000000..0315573b --- /dev/null +++ b/images/neurodesk/neurodesk-fsl--6.0.7.8.simg @@ -0,0 +1 @@ +../../.git/annex/objects/3M/XV/MD5E-s6021951488--4caa7b2d5a030459d6716a736a0e1896.8.simg/MD5E-s6021951488--4caa7b2d5a030459d6716a736a0e1896.8.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-micapipe--v0.2.3.simg b/images/neurodesk/neurodesk-micapipe--v0.2.3.simg new file mode 120000 index 00000000..b625c860 --- /dev/null +++ b/images/neurodesk/neurodesk-micapipe--v0.2.3.simg @@ -0,0 +1 @@ +../../.git/annex/objects/M7/8p/MD5E-s21323853824--fb983d43a91b17d58e8dee958fa40403.3.simg/MD5E-s21323853824--fb983d43a91b17d58e8dee958fa40403.3.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-niimath--1.0.0.simg b/images/neurodesk/neurodesk-niimath--1.0.0.simg new file mode 120000 index 00000000..443a9d6b --- /dev/null +++ b/images/neurodesk/neurodesk-niimath--1.0.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/Vx/p4/MD5E-s9003008--1de1c80a723baf7e9a447e2487d4fa1d.0.simg/MD5E-s9003008--1de1c80a723baf7e9a447e2487d4fa1d.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-qsmxt--7.2.0.simg b/images/neurodesk/neurodesk-qsmxt--7.2.0.simg new file mode 120000 index 00000000..11464599 --- /dev/null +++ b/images/neurodesk/neurodesk-qsmxt--7.2.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/W5/9J/MD5E-s3993894912--f29e4546d1ba5efe406b65c6b3887e5b.0.simg/MD5E-s3993894912--f29e4546d1ba5efe406b65c6b3887e5b.0.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-qsmxt--7.2.1.simg b/images/neurodesk/neurodesk-qsmxt--7.2.1.simg new file mode 120000 index 00000000..3bec1149 --- /dev/null +++ b/images/neurodesk/neurodesk-qsmxt--7.2.1.simg @@ -0,0 +1 @@ +../../.git/annex/objects/G7/V6/MD5E-s3992567808--4182e6d80de0c08eb8360a5471628373.1.simg/MD5E-s3992567808--4182e6d80de0c08eb8360a5471628373.1.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-spinalcordtoolbox--6.4.simg b/images/neurodesk/neurodesk-spinalcordtoolbox--6.4.simg new file mode 120000 index 00000000..ca4ade8e --- /dev/null +++ b/images/neurodesk/neurodesk-spinalcordtoolbox--6.4.simg @@ -0,0 +1 @@ +../../.git/annex/objects/p4/Mx/MD5E-s3221381120--90c115d45e86ea478889f2f46dfed03a.4.simg/MD5E-s3221381120--90c115d45e86ea478889f2f46dfed03a.4.simg \ No newline at end of file diff --git a/images/neurodesk/neurodesk-vmtk--1.5.0.simg b/images/neurodesk/neurodesk-vmtk--1.5.0.simg new file mode 120000 index 00000000..a1860e50 --- /dev/null +++ b/images/neurodesk/neurodesk-vmtk--1.5.0.simg @@ -0,0 +1 @@ +../../.git/annex/objects/JX/V8/MD5E-s1985216512--3d2c8f1a6a76e1f0c1247e8c28f4f153.0.simg/MD5E-s1985216512--3d2c8f1a6a76e1f0c1247e8c28f4f153.0.simg \ No newline at end of file diff --git a/images/nipy/Singularity.nipy-heudiconv--1.2.0 b/images/nipy/Singularity.nipy-heudiconv--1.2.0 new file mode 100644 index 00000000..46dccb2e --- /dev/null +++ b/images/nipy/Singularity.nipy-heudiconv--1.2.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipy/heudiconv:1.2.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/nipy/Singularity.nipy-heudiconv--1.3.0 b/images/nipy/Singularity.nipy-heudiconv--1.3.0 new file mode 100644 index 00000000..5ab89825 --- /dev/null +++ b/images/nipy/Singularity.nipy-heudiconv--1.3.0 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipy/heudiconv:1.3.0 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/nipy/Singularity.nipy-heudiconv--1.3.1 b/images/nipy/Singularity.nipy-heudiconv--1.3.1 new file mode 100644 index 00000000..cc7054cc --- /dev/null +++ b/images/nipy/Singularity.nipy-heudiconv--1.3.1 @@ -0,0 +1,18 @@ +# +# Automagically prepared for ReproNim/containers distribution. +# See http://github.com/ReproNim/containers for more info +# +Bootstrap: docker +From: nipy/heudiconv:1.3.1 + +%post + +# Create commonly present root directories to avoid need in overlays not supported +# on older systems +mkdir -p /ihome /data /data2 /zfs /isi /dartfs /dartfs-hpc + +%environment +export LANG="C.UTF-8" +export LC_ALL="C.UTF-8" + +# TODO: Take advantage of the fact that it is a bids-app somehow? diff --git a/images/nipy/nipy-heudiconv--1.2.0.sing b/images/nipy/nipy-heudiconv--1.2.0.sing new file mode 120000 index 00000000..1c3fceea --- /dev/null +++ b/images/nipy/nipy-heudiconv--1.2.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/6F/7G/MD5E-s529829919--b163f203737091f3036b5d91a3a49db1.0.sing/MD5E-s529829919--b163f203737091f3036b5d91a3a49db1.0.sing \ No newline at end of file diff --git a/images/nipy/nipy-heudiconv--1.3.0.sing b/images/nipy/nipy-heudiconv--1.3.0.sing new file mode 120000 index 00000000..019a6ca8 --- /dev/null +++ b/images/nipy/nipy-heudiconv--1.3.0.sing @@ -0,0 +1 @@ +../../.git/annex/objects/wm/zk/MD5E-s528433183--bccd6519ff6cbde4f9ade6aa134edf79.0.sing/MD5E-s528433183--bccd6519ff6cbde4f9ade6aa134edf79.0.sing \ No newline at end of file diff --git a/images/nipy/nipy-heudiconv--1.3.1.sing b/images/nipy/nipy-heudiconv--1.3.1.sing new file mode 120000 index 00000000..38a0ec47 --- /dev/null +++ b/images/nipy/nipy-heudiconv--1.3.1.sing @@ -0,0 +1 @@ +../../.git/annex/objects/8K/9X/MD5E-s529543199--4375f33e818dc9e26397ad26edcfc138.1.sing/MD5E-s529543199--4375f33e818dc9e26397ad26edcfc138.1.sing \ No newline at end of file diff --git a/scripts/create_singularities b/scripts/create_singularities index ed8565c3..b65e5402 100755 --- a/scripts/create_singularities +++ b/scripts/create_singularities @@ -299,7 +299,7 @@ export LC_ALL="C.UTF-8" if self.githubids and githubid not in self.githubids: log.info("skip %s", githubid) return - if dockerhubid in ("djarecka/fmriprep_fake", "pennlinc/toy_bids_app"): + if dockerhubid in ("djarecka/fmriprep_fake", "pennlinc/toy_bids_app", "nipreps/fmripost-aroma", "nipreps/fmripost-phase", "nipreps/fmripost-rapidtide"): log.info("TEMP TODO skip %s due to odd OCI issue ATM with old singularity", dockerhubid) return log.info("%s <- docker %s", family, dockerhubid) @@ -411,7 +411,7 @@ def main(push: bool, githubids: list[str]|None) -> None: sys.exit(1) r = requests.get( - "https://raw.githubusercontent.com/BIDS-Apps/bids-apps.github.io/master/_config.yml" + "https://raw.githubusercontent.com/bids-standard/bids-website/main/data/tools/apps.yml" ) r.raise_for_status() for line in r.text.splitlines():