From c7c33aa346e7396779ddf823a90434b0e46afb79 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Sat, 31 Aug 2024 08:32:35 -0400 Subject: [PATCH 01/77] Fixed permissions for bids-mriqc--24.0.2.sing too now (ran manually) --- images/bids/Singularity.bids-mriqc--24.0.2 | 4 ++++ images/bids/bids-mriqc--24.0.2.sing | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) 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/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 From 33f7886bd3f569c8ee891adaa2800b14233aebb7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:11:50 -0400 Subject: [PATCH 02/77] Adding recipe&image for bids-nibabies--24.0.1 --- images/bids/Singularity.bids-nibabies--24.0.1 | 18 ++++++++++++++++++ images/bids/bids-nibabies--24.0.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-nibabies--24.0.1 create mode 120000 images/bids/bids-nibabies--24.0.1.sing 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/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 From 4b86ebe75f3cfc804be739f35b63116ea8d3a1e7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:11:53 -0400 Subject: [PATCH 03/77] [DATALAD] Configure containerized environment 'bids-nibabies' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 72e40049..4f9c4a5c 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--24.0.1.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-nirodents"] image = images/bids/bids-nirodents--0.2.1.sing From accd14b85b2bd4a1e9af9883b9b6c476be8fa08d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:19:23 -0400 Subject: [PATCH 04/77] Adding recipe&image for bids-qsiprep--0.23.0 --- images/bids/Singularity.bids-qsiprep--0.23.0 | 18 ++++++++++++++++++ images/bids/bids-qsiprep--0.23.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-qsiprep--0.23.0 create mode 120000 images/bids/bids-qsiprep--0.23.0.sing 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/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 From 4004b53c56675c8cedc85efd3551038cf23383de Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:19:26 -0400 Subject: [PATCH 05/77] [DATALAD] Configure containerized environment 'bids-qsiprep' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 4f9c4a5c..6937a6bc 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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 From c47326738e1dd8a8a12c4e2bb2531d627a3621f6 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:21:28 -0400 Subject: [PATCH 06/77] [DATALAD] Configure containerized environment 'neurodesk-qsmxt' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 6937a6bc..919af64a 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--7.2.0.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-physio"] image = images/neurodesk/neurodesk-physio--r2021a.simg From 71a5a66c2686864653e53f065465bac5eb1dda93 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:21:31 -0400 Subject: [PATCH 07/77] [DATALAD] Configure containerized environment 'neurodesk-niimath' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index 919af64a..30563734 100644 --- a/.datalad/config +++ b/.datalad/config @@ -483,3 +483,6 @@ [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} From b9e2224a0e2bd984cfd4d1e7e4612972c10802c8 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 00:21:33 -0400 Subject: [PATCH 08/77] Add 2 NeuroDesk images with 2 registered --- images/neurodesk/neurodesk-niimath--1.0.0.simg | 1 + images/neurodesk/neurodesk-qsmxt--7.2.0.simg | 1 + 2 files changed, 2 insertions(+) create mode 120000 images/neurodesk/neurodesk-niimath--1.0.0.simg create mode 120000 images/neurodesk/neurodesk-qsmxt--7.2.0.simg 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 From d5759251da471f927e76fbb290e6f70c42243408 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 15:05:44 -0400 Subject: [PATCH 09/77] Adding recipe&image for bids-validator--1.14.11 --- .../bids/Singularity.bids-validator--1.14.11 | 18 ++++++++++++++++++ images/bids/bids-validator--1.14.11.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-validator--1.14.11 create mode 120000 images/bids/bids-validator--1.14.11.sing 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/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 From bceb41f6add142da3687075b37ff117d4172d5a0 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 3 Sep 2024 15:05:47 -0400 Subject: [PATCH 10/77] [DATALAD] Configure containerized environment 'bids-validator' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 30563734..357f41b8 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.14.11.sing [datalad "containers.neuronets-kwyk"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} image = images/neuronets/neuronets-kwyk--0.5.0-gpu.sing From ee6520d32e1765a8de83c1a2c7644cb726fae834 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 10 Sep 2024 00:13:19 -0400 Subject: [PATCH 11/77] Adding recipe&image for bids-xcp-d--0.9.0 --- images/bids/Singularity.bids-xcp-d--0.9.0 | 18 ++++++++++++++++++ images/bids/bids-xcp-d--0.9.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-xcp-d--0.9.0 create mode 120000 images/bids/bids-xcp-d--0.9.0.sing 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/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 From f7386c7df3fbec10a0087713eb2c1c4961aacd75 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 10 Sep 2024 00:13:21 -0400 Subject: [PATCH 12/77] [DATALAD] Configure containerized environment 'bids-xcp-d' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 357f41b8..8c494140 100644 --- a/.datalad/config +++ b/.datalad/config @@ -424,7 +424,7 @@ 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--0.9.0.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-aslprep"] image = images/bids/bids-aslprep--0.7.2.sing From 33871a57de1380095a4ad787fe4a5ab1f1e73809 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 10 Sep 2024 00:13:55 -0400 Subject: [PATCH 13/77] Adding recipe&image for bids-validator--1.14.12 --- .../bids/Singularity.bids-validator--1.14.12 | 18 ++++++++++++++++++ images/bids/bids-validator--1.14.12.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-validator--1.14.12 create mode 120000 images/bids/bids-validator--1.14.12.sing 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/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 From 929aab01819fd4d08d70c25bc2519f7120ac8f79 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 10 Sep 2024 00:13:58 -0400 Subject: [PATCH 14/77] [DATALAD] Configure containerized environment 'bids-validator' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 8c494140..6c43a684 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.14.11.sing + image = images/bids/bids-validator--1.14.12.sing [datalad "containers.neuronets-kwyk"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} image = images/neuronets/neuronets-kwyk--0.5.0-gpu.sing From 919e5423d76e69a1ad3a221597d0954250f232d4 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 10 Sep 2024 18:18:23 -0400 Subject: [PATCH 15/77] Adding recipe&image for bids-bibsnet--3.4.2 --- images/bids/Singularity.bids-bibsnet--3.4.2 | 18 ++++++++++++++++++ images/bids/bids-bibsnet--3.4.2.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-bibsnet--3.4.2 create mode 120000 images/bids/bids-bibsnet--3.4.2.sing 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/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 From 1868fd1ad9158e1467d886ff66f9493291fce99d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 10 Sep 2024 18:18:26 -0400 Subject: [PATCH 16/77] [DATALAD] Configure containerized environment 'bids-bibsnet' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 6c43a684..a6db4aa7 100644 --- a/.datalad/config +++ b/.datalad/config @@ -469,7 +469,7 @@ 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 From 6f248d917003e7dfb86a81d4f9eb9716c3644de2 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 09:51:34 -0400 Subject: [PATCH 17/77] Listing of apps moved Thanks @Remi-Gau for the heads up Closes https://github.com/ReproNim/containers/issues/129 --- scripts/create_singularities | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/create_singularities b/scripts/create_singularities index ed8565c3..001a76dd 100755 --- a/scripts/create_singularities +++ b/scripts/create_singularities @@ -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(): From 9b0570fda7a8e9fa3b1735946faffbd4e18069c9 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 09:52:56 -0400 Subject: [PATCH 18/77] Adding recipe&image for bids-bidspm--4.0.0 --- images/bids/Singularity.bids-bidspm--4.0.0 | 18 ++++++++++++++++++ images/bids/bids-bidspm--4.0.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-bidspm--4.0.0 create mode 120000 images/bids/bids-bidspm--4.0.0.sing 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/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 From 167d9ef4bbb81d56738b803ef24c0f421150b0e9 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 09:52:59 -0400 Subject: [PATCH 19/77] [DATALAD] Configure containerized environment 'bids-bidspm' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index a6db4aa7..42d3d150 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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 From 8e35c0b442e8468dd26af87e02dd9e55d4d8eaa3 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 10:04:13 -0400 Subject: [PATCH 20/77] one more bids app to skip for now --- scripts/create_singularities | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/create_singularities b/scripts/create_singularities index 001a76dd..8cf88a99 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"): log.info("TEMP TODO skip %s due to odd OCI issue ATM with old singularity", dockerhubid) return log.info("%s <- docker %s", family, dockerhubid) From bb6737cd9e9d81341398c66b67307d8022fa9200 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 11:17:57 -0400 Subject: [PATCH 21/77] skip nipreps/fmripost-phase too for now --- scripts/create_singularities | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/create_singularities b/scripts/create_singularities index 8cf88a99..5f1781fb 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", "nipreps/fmripost-aroma"): + if dockerhubid in ("djarecka/fmriprep_fake", "pennlinc/toy_bids_app", "nipreps/fmripost-aroma", "nipreps/fmripost-phase"): log.info("TEMP TODO skip %s due to odd OCI issue ATM with old singularity", dockerhubid) return log.info("%s <- docker %s", family, dockerhubid) From c434de082eb4094055569d2fffe7e230cd4c58bf Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 12:55:06 -0400 Subject: [PATCH 22/77] skip nipreps/fmripost-rapidtide too for now too --- scripts/create_singularities | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/create_singularities b/scripts/create_singularities index 5f1781fb..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", "nipreps/fmripost-aroma", "nipreps/fmripost-phase"): + 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) From 8f88721e0904a1b0e6726ae37e3dc034decc5af5 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:01:05 -0400 Subject: [PATCH 23/77] Adding recipe&image for bids-xcp-d--0.9.1 --- images/bids/Singularity.bids-xcp-d--0.9.1 | 18 ++++++++++++++++++ images/bids/bids-xcp-d--0.9.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-xcp-d--0.9.1 create mode 120000 images/bids/bids-xcp-d--0.9.1.sing 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-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 From 975c3a8c8f5b29a5ed1e25bc3413278c190ef411 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:01:08 -0400 Subject: [PATCH 24/77] [DATALAD] Configure containerized environment 'bids-xcp-d' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 42d3d150..1539ebda 100644 --- a/.datalad/config +++ b/.datalad/config @@ -424,7 +424,7 @@ 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--0.9.0.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 From 816819a4217a0cd9db3e6740e0766c7b1c029eea Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:08:58 -0400 Subject: [PATCH 25/77] Adding recipe&image for bids-qsirecon--unstable --- .../bids/Singularity.bids-qsirecon--unstable | 18 ++++++++++++++++++ images/bids/bids-qsirecon--unstable.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-qsirecon--unstable create mode 120000 images/bids/bids-qsirecon--unstable.sing 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/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 From 1dd257768bcc35d737a1cab77534e1789a874cc4 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:09:01 -0400 Subject: [PATCH 26/77] [DATALAD] Configure containerized environment 'bids-qsirecon' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index 1539ebda..cb3fd32b 100644 --- a/.datalad/config +++ b/.datalad/config @@ -486,3 +486,6 @@ [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--unstable.sing + cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} From f68bed0d23a9f8e55bf078a3aa6a0ef68a740d96 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:11:53 -0400 Subject: [PATCH 27/77] Adding recipe&image for bids-reproa--0.2.1 --- images/bids/Singularity.bids-reproa--0.2.1 | 18 ++++++++++++++++++ images/bids/bids-reproa--0.2.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-reproa--0.2.1 create mode 120000 images/bids/bids-reproa--0.2.1.sing 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/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 From b80d9f19ce60a521836aa854e045a32eba5b6928 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:11:56 -0400 Subject: [PATCH 28/77] [DATALAD] Configure containerized environment 'bids-reproa' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index cb3fd32b..1e204e95 100644 --- a/.datalad/config +++ b/.datalad/config @@ -489,3 +489,6 @@ [datalad "containers.bids-qsirecon"] image = images/bids/bids-qsirecon--unstable.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} From 7ce7f1f7fa20e153e784604f362e5e7558f9f1dc Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:12:32 -0400 Subject: [PATCH 29/77] Adding recipe&image for bids-validator--1.14.13 --- .../bids/Singularity.bids-validator--1.14.13 | 18 ++++++++++++++++++ images/bids/bids-validator--1.14.13.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-validator--1.14.13 create mode 120000 images/bids/bids-validator--1.14.13.sing 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/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 From 68c1de6f1f4e720c363382e25cf48e6ae2968e5a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:12:35 -0400 Subject: [PATCH 30/77] [DATALAD] Configure containerized environment 'bids-validator' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 1e204e95..6bf00359 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.14.12.sing + image = images/bids/bids-validator--1.14.13.sing [datalad "containers.neuronets-kwyk"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} image = images/neuronets/neuronets-kwyk--0.5.0-gpu.sing From e7724bf9bb3fac157ac633f13db85b1c22d0d31e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:17:16 -0400 Subject: [PATCH 31/77] [DATALAD] Configure containerized environment 'neurodesk-fsl' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 6bf00359..a1579d5d 100644 --- a/.datalad/config +++ b/.datalad/config @@ -298,7 +298,7 @@ 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--6.0.7.8.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-freesurfer"] image = images/neurodesk/neurodesk-freesurfer--7.4.1.simg From 5e28eb82798d5749766ce97609572bc94973e2a1 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 13 Sep 2024 13:17:17 -0400 Subject: [PATCH 32/77] Add 1 NeuroDesk images with 1 registered --- images/neurodesk/neurodesk-fsl--6.0.7.8.simg | 1 + 1 file changed, 1 insertion(+) create mode 120000 images/neurodesk/neurodesk-fsl--6.0.7.8.simg 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 From 49d6345309a71d2e79ff34b60b76f34dcaff23e7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 17 Sep 2024 00:09:43 -0400 Subject: [PATCH 33/77] Adding recipe&image for bids-fmriprep--24.1.0 --- images/bids/Singularity.bids-fmriprep--24.1.0 | 18 ++++++++++++++++++ images/bids/bids-fmriprep--24.1.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-fmriprep--24.1.0 create mode 120000 images/bids/bids-fmriprep--24.1.0.sing 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/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 From 51e756be0c67b3188f072da148c91fadc43e9cbb Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 17 Sep 2024 00:09:46 -0400 Subject: [PATCH 34/77] [DATALAD] Configure containerized environment 'bids-fmriprep' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index a1579d5d..ef9a108c 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--24.1.0.sing [datalad "containers.bids-freesurfer"] cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} image = images/bids/bids-freesurfer--7.4.1-unstable.sing From 3df37f3253c04cfbee1ce0ecaf79cd571f54a017 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 17 Sep 2024 00:11:26 -0400 Subject: [PATCH 35/77] Adding recipe&image for nipy-heudiconv--1.2.0 --- images/nipy/Singularity.nipy-heudiconv--1.2.0 | 18 ++++++++++++++++++ images/nipy/nipy-heudiconv--1.2.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/nipy/Singularity.nipy-heudiconv--1.2.0 create mode 120000 images/nipy/nipy-heudiconv--1.2.0.sing 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/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 From 79f9bb1dd62f64474e91ba97629d47a13bae5bbd Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 17 Sep 2024 00:11:29 -0400 Subject: [PATCH 36/77] [DATALAD] Configure containerized environment 'nipy-heudiconv' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index ef9a108c..4e465db3 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.2.0.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 From 5dcfa05b742111b26697eac4f9abaf4d2c107734 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 17 Sep 2024 22:08:02 -0400 Subject: [PATCH 37/77] [DATALAD] Configure containerized environment 'neurodesk-aslprep' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 4e465db3..76943a26 100644 --- a/.datalad/config +++ b/.datalad/config @@ -361,7 +361,7 @@ 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 From 280ad873c12a311b50a56dcfe546ceccae715805 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 17 Sep 2024 22:08:03 -0400 Subject: [PATCH 38/77] Add 1 NeuroDesk images with 1 registered --- images/neurodesk/neurodesk-aslprep--0.7.2.simg | 1 + 1 file changed, 1 insertion(+) create mode 120000 images/neurodesk/neurodesk-aslprep--0.7.2.simg 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 From 19ec7d54a1739edda2e08af2eba989b201621735 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:08:27 -0400 Subject: [PATCH 39/77] [DATALAD] Configure containerized environment 'neurodesk-spinalcordtoolbox' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 76943a26..4d5bddb4 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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 From e8114f8c0775f47576605a70387519ca93fb515a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:18:45 -0400 Subject: [PATCH 40/77] [DATALAD] Configure containerized environment 'neurodesk-micapipe' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index 4d5bddb4..5c52da3c 100644 --- a/.datalad/config +++ b/.datalad/config @@ -492,3 +492,6 @@ [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} From 512d37d28f6f8ad029ff0e9efa2bcec59548ed71 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:18:53 -0400 Subject: [PATCH 41/77] [DATALAD] Configure containerized environment 'neurodesk-dcm2niix' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index 5c52da3c..a6939c20 100644 --- a/.datalad/config +++ b/.datalad/config @@ -495,3 +495,6 @@ [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} From d981d0431eb1ace6c622260f60eed24aae68e59e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:19:52 -0400 Subject: [PATCH 42/77] [DATALAD] Configure containerized environment 'neurodesk-brainnetviewer' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index a6939c20..283b07de 100644 --- a/.datalad/config +++ b/.datalad/config @@ -498,3 +498,6 @@ [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} From da58bd6da953c8168ea86b63f77b4c629bb9dafe Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:20:02 -0400 Subject: [PATCH 43/77] [DATALAD] Configure containerized environment 'neurodesk-ants' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 283b07de..8e05c95f 100644 --- a/.datalad/config +++ b/.datalad/config @@ -364,7 +364,7 @@ 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 From 495d1700b769a9090219159626aa5acc9fddb947 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:23:26 -0400 Subject: [PATCH 44/77] [DATALAD] Configure containerized environment 'neurodesk-afni' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 8e05c95f..d0fc9740 100644 --- a/.datalad/config +++ b/.datalad/config @@ -370,7 +370,7 @@ 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--24.2.07.simg cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.neurodesk-mfcsc"] image = images/neurodesk/neurodesk-mfcsc--1.1.simg From 67bf000890443a5c58866bbc02a2e81117ce8d68 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 00:23:27 -0400 Subject: [PATCH 45/77] Add 6 NeuroDesk images with 6 registered --- images/neurodesk/neurodesk-afni--24.2.07.simg | 1 + images/neurodesk/neurodesk-ants--2.5.3.simg | 1 + images/neurodesk/neurodesk-brainnetviewer--1.7.20191031.simg | 1 + images/neurodesk/neurodesk-dcm2niix--v1.0.20240202.simg | 1 + images/neurodesk/neurodesk-micapipe--v0.2.3.simg | 1 + images/neurodesk/neurodesk-spinalcordtoolbox--6.4.simg | 1 + 6 files changed, 6 insertions(+) create mode 120000 images/neurodesk/neurodesk-afni--24.2.07.simg create mode 120000 images/neurodesk/neurodesk-ants--2.5.3.simg create mode 120000 images/neurodesk/neurodesk-brainnetviewer--1.7.20191031.simg create mode 120000 images/neurodesk/neurodesk-dcm2niix--v1.0.20240202.simg create mode 120000 images/neurodesk/neurodesk-micapipe--v0.2.3.simg create mode 120000 images/neurodesk/neurodesk-spinalcordtoolbox--6.4.simg 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-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-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-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-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 From e6119bdcb4e38199f9d7009656aa513679cfca88 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 22:07:00 -0400 Subject: [PATCH 46/77] Adding recipe&image for nipy-heudiconv--1.3.0 --- images/nipy/Singularity.nipy-heudiconv--1.3.0 | 18 ++++++++++++++++++ images/nipy/nipy-heudiconv--1.3.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/nipy/Singularity.nipy-heudiconv--1.3.0 create mode 120000 images/nipy/nipy-heudiconv--1.3.0.sing 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/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 From 85544a19df18c698c2c00fca353c2a60682b0056 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 1 Oct 2024 22:07:02 -0400 Subject: [PATCH 47/77] [DATALAD] Configure containerized environment 'nipy-heudiconv' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index d0fc9740..05ddc440 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.2.0.sing + image = images/nipy/nipy-heudiconv--1.3.0.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 From 58b335f3f96f0bdb1fc76fd59144dcdb5d26295e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:10:32 -0400 Subject: [PATCH 48/77] Adding recipe&image for bids-nibabies--24.1.0 --- images/bids/Singularity.bids-nibabies--24.1.0 | 18 ++++++++++++++++++ images/bids/bids-nibabies--24.1.0.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-nibabies--24.1.0 create mode 120000 images/bids/bids-nibabies--24.1.0.sing 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/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 From b23323e449dd3417b706b24cb5d4ef2549e9e3a0 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:10:35 -0400 Subject: [PATCH 49/77] [DATALAD] Configure containerized environment 'bids-nibabies' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 05ddc440..7cb5e8ea 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--24.0.1.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 From 4bc87380c36e86acbdf664fa7766150483066216 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:16:52 -0400 Subject: [PATCH 50/77] Adding recipe&image for bids-qsirecon--0.23.1 --- images/bids/Singularity.bids-qsirecon--0.23.1 | 18 ++++++++++++++++++ images/bids/bids-qsirecon--0.23.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-qsirecon--0.23.1 create mode 120000 images/bids/bids-qsirecon--0.23.1.sing 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/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 From 86fe31838c10876098fe7292e0e8b1b5e33b5e14 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:16:54 -0400 Subject: [PATCH 51/77] [DATALAD] Configure containerized environment 'bids-qsirecon' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 7cb5e8ea..277ec3b2 100644 --- a/.datalad/config +++ b/.datalad/config @@ -487,7 +487,7 @@ 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--unstable.sing + image = images/bids/bids-qsirecon--0.23.1.sing cmdexec = {img_dspath}/scripts/singularity_cmd run {img} {cmd} [datalad "containers.bids-reproa"] image = images/bids/bids-reproa--0.2.1.sing From 69f5b34a3d0ed7e998dcef388404ae2bc9b9fb72 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:18:25 -0400 Subject: [PATCH 52/77] [DATALAD] Configure containerized environment 'neurodesk-fmriprep' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 277ec3b2..ce81cfd8 100644 --- a/.datalad/config +++ b/.datalad/config @@ -304,7 +304,7 @@ 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 From e16784cb5208ba2d3e4263dde0ef6e44f1ba638a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:18:45 -0400 Subject: [PATCH 53/77] [DATALAD] Configure containerized environment 'neurodesk-brainlifecli' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index ce81cfd8..e9c2ffd8 100644 --- a/.datalad/config +++ b/.datalad/config @@ -501,3 +501,6 @@ [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} From 6749796db605fc9616001af532553586bfeb476e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:19:15 -0400 Subject: [PATCH 54/77] [DATALAD] Configure containerized environment 'neurodesk-bidscoin' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index e9c2ffd8..ecef900d 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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 From facd84cef0c531ba524f27f55ea5f8df0a558e18 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:23:20 -0400 Subject: [PATCH 55/77] [DATALAD] Configure containerized environment 'neurodesk-afni' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index ecef900d..76564b7f 100644 --- a/.datalad/config +++ b/.datalad/config @@ -370,7 +370,7 @@ 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--24.2.07.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 From e39b1f34e988f6718f2669f890a1dfeddf8f64ac Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 8 Oct 2024 00:23:21 -0400 Subject: [PATCH 56/77] Add 4 NeuroDesk images with 4 registered --- images/neurodesk/neurodesk-afni--24.3.00.simg | 1 + images/neurodesk/neurodesk-bidscoin--4.4.0.simg | 1 + images/neurodesk/neurodesk-brainlifecli--1.7.0.simg | 1 + images/neurodesk/neurodesk-fmriprep--24.1.0.simg | 1 + 4 files changed, 4 insertions(+) create mode 120000 images/neurodesk/neurodesk-afni--24.3.00.simg create mode 120000 images/neurodesk/neurodesk-bidscoin--4.4.0.simg create mode 120000 images/neurodesk/neurodesk-brainlifecli--1.7.0.simg create mode 120000 images/neurodesk/neurodesk-fmriprep--24.1.0.simg 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-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-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 From b85d37d190ccb451b7ae8c4c6c0d1bbcea1c04bb Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 00:08:42 -0400 Subject: [PATCH 57/77] Adding recipe&image for bids-fmriprep--24.1.1 --- images/bids/Singularity.bids-fmriprep--24.1.1 | 18 ++++++++++++++++++ images/bids/bids-fmriprep--24.1.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-fmriprep--24.1.1 create mode 120000 images/bids/bids-fmriprep--24.1.1.sing 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/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 From 0f3d4f9d1951fd64cffbebe3c86cdf5045b3f201 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 00:08:45 -0400 Subject: [PATCH 58/77] [DATALAD] Configure containerized environment 'bids-fmriprep' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 76564b7f..7fa26419 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--24.1.0.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 From d444b166af88c2c50166f846fcdc83e956868ffb Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 00:12:58 -0400 Subject: [PATCH 59/77] Adding recipe&image for bids-aslprep--0.7.3 --- images/bids/Singularity.bids-aslprep--0.7.3 | 18 ++++++++++++++++++ images/bids/bids-aslprep--0.7.3.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-aslprep--0.7.3 create mode 120000 images/bids/bids-aslprep--0.7.3.sing 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/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 From fb525f8d29691f9eee7e516cd97ff5dcdee5ac78 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 00:13:00 -0400 Subject: [PATCH 60/77] [DATALAD] Configure containerized environment 'bids-aslprep' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 7fa26419..5ba472ed 100644 --- a/.datalad/config +++ b/.datalad/config @@ -427,7 +427,7 @@ 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 From 5ce4d25e511da57626d7d24c85c5a4b44590dc59 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 03:05:23 -0400 Subject: [PATCH 61/77] [DATALAD] Configure containerized environment 'neurodesk-dsistudio' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 5ba472ed..adf61157 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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 From 4eb9545521a2520bc2c21fe5ecbbca2f37e1125c Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 03:05:24 -0400 Subject: [PATCH 62/77] Add 1 NeuroDesk images with 1 registered --- images/neurodesk/neurodesk-dsistudio--2024.06.12.simg | 1 + 1 file changed, 1 insertion(+) create mode 120000 images/neurodesk/neurodesk-dsistudio--2024.06.12.simg 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 From 767549cdd0baeb476f0bf96b07521a7ec14fa538 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 04:06:01 -0400 Subject: [PATCH 63/77] [DATALAD] Configure containerized environment 'neurodesk-vmtk' --- .datalad/config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.datalad/config b/.datalad/config index adf61157..68cac029 100644 --- a/.datalad/config +++ b/.datalad/config @@ -504,3 +504,6 @@ [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} From 8f08f307090bb91cd5fc52b7d3810586ca58ed67 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 04:06:02 -0400 Subject: [PATCH 64/77] Add 1 NeuroDesk images with 1 registered --- images/neurodesk/neurodesk-vmtk--1.5.0.simg | 1 + 1 file changed, 1 insertion(+) create mode 120000 images/neurodesk/neurodesk-vmtk--1.5.0.simg 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 From c69404f855b5c54c3cbaa8e2357db7068e502c54 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 19:05:42 -0400 Subject: [PATCH 65/77] Adding recipe&image for bids-validator--1.14.14 --- .../bids/Singularity.bids-validator--1.14.14 | 18 ++++++++++++++++++ images/bids/bids-validator--1.14.14.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-validator--1.14.14 create mode 120000 images/bids/bids-validator--1.14.14.sing 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/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 From 5c412bac121959e4f141f2730ea43c1627057aeb Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 15 Oct 2024 19:05:49 -0400 Subject: [PATCH 66/77] [DATALAD] Configure containerized environment 'bids-validator' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 68cac029..90cdd081 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.14.13.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 From f6cfbd5f53185ae4b86311901523674654d3f4e7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 22 Oct 2024 00:11:31 -0400 Subject: [PATCH 67/77] Adding recipe&image for bids-qsirecon--0.23.2 --- images/bids/Singularity.bids-qsirecon--0.23.2 | 18 ++++++++++++++++++ images/bids/bids-qsirecon--0.23.2.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-qsirecon--0.23.2 create mode 120000 images/bids/bids-qsirecon--0.23.2.sing 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/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 From e3fae89b4ef4ca4982c22c6792d7ba55ecd23d9b Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 22 Oct 2024 00:11:34 -0400 Subject: [PATCH 68/77] [DATALAD] Configure containerized environment 'bids-qsirecon' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 90cdd081..68070517 100644 --- a/.datalad/config +++ b/.datalad/config @@ -487,7 +487,7 @@ 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--0.23.1.sing + 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 From ac5b8c9cb48020073feca7410e51c071b8fb3ca3 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 22 Oct 2024 00:15:42 -0400 Subject: [PATCH 69/77] [DATALAD] Configure containerized environment 'neurodesk-fsl' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 68070517..8938f20d 100644 --- a/.datalad/config +++ b/.datalad/config @@ -298,7 +298,7 @@ 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--6.0.7.8.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 From e8f3458b40fb0dce0415df39a890db0021ae152b Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 22 Oct 2024 00:15:42 -0400 Subject: [PATCH 70/77] Add 1 NeuroDesk images with 1 registered --- images/neurodesk/neurodesk-fsl--6.0.7.14.simg | 1 + 1 file changed, 1 insertion(+) create mode 120000 images/neurodesk/neurodesk-fsl--6.0.7.14.simg 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 From 956ee9ba1db4eb6e5f813b6110455918d9b660c0 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 22 Oct 2024 19:08:05 -0400 Subject: [PATCH 71/77] [DATALAD] Configure containerized environment 'neurodesk-qsmxt' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 8938f20d..31cf3640 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--7.2.0.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 From 50d1c91f5ab167a30d2bdc912d278310f22200d8 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 22 Oct 2024 19:08:06 -0400 Subject: [PATCH 72/77] Add 1 NeuroDesk images with 1 registered --- images/neurodesk/neurodesk-qsmxt--7.2.1.simg | 1 + 1 file changed, 1 insertion(+) create mode 120000 images/neurodesk/neurodesk-qsmxt--7.2.1.simg 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 From 10f041e8c19336f2a3c2438e844817aa83f0581f Mon Sep 17 00:00:00 2001 From: Isaac To Date: Sun, 27 Oct 2024 16:04:10 -0700 Subject: [PATCH 73/77] fix: Correct typo in link to CI badge and workflow result --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From e41c66887aab593ed65cd2e0daf1b9d0eea7650e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 29 Oct 2024 00:20:30 -0400 Subject: [PATCH 74/77] Adding recipe&image for bids-petdeface--0.2.1 --- images/bids/Singularity.bids-petdeface--0.2.1 | 18 ++++++++++++++++++ images/bids/bids-petdeface--0.2.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/bids/Singularity.bids-petdeface--0.2.1 create mode 120000 images/bids/bids-petdeface--0.2.1.sing 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/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 From 7f67749189858b4fbcef4849061417a99d289b77 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 29 Oct 2024 00:20:33 -0400 Subject: [PATCH 75/77] [DATALAD] Configure containerized environment 'bids-petdeface' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 31cf3640..8566e254 100644 --- a/.datalad/config +++ b/.datalad/config @@ -472,7 +472,7 @@ 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 From 41796c053534eac48cf3ca015b2a47b497546c8f Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 29 Oct 2024 00:21:27 -0400 Subject: [PATCH 76/77] Adding recipe&image for nipy-heudiconv--1.3.1 --- images/nipy/Singularity.nipy-heudiconv--1.3.1 | 18 ++++++++++++++++++ images/nipy/nipy-heudiconv--1.3.1.sing | 1 + 2 files changed, 19 insertions(+) create mode 100644 images/nipy/Singularity.nipy-heudiconv--1.3.1 create mode 120000 images/nipy/nipy-heudiconv--1.3.1.sing 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--1.3.1.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 From 85bf80033c9459e6f193fbc92defb113755edc4b Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 29 Oct 2024 00:21:30 -0400 Subject: [PATCH 77/77] [DATALAD] Configure containerized environment 'nipy-heudiconv' --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 8566e254..83c7497d 100644 --- a/.datalad/config +++ b/.datalad/config @@ -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--1.3.0.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