removing bidscoin from this container to remove duplicated maintenanc…

…e effort, addressing #596
NeuroDesk · Feb 20, 2024 · c981d4f · c981d4f
1 parent 2f72d05
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diff --git a/recipes/bidstools/README.md b/recipes/bidstools/README.md
@@ -6,22 +6,6 @@ Contains a collection of tools useful for DICOM to BIDS conversion
 Tools included:
 ```
 dcm2niix: https://github.com/rordenlab/dcm2niix
-bidscoin: https://bidscoin.readthedocs.io
-    bidscoin
-    bidscoiner
-    bidseditor
-    bidsmapper
-    bidsparticipants
-    deface
-    dicomsort
-    echocombine
-    medeface
-    physio2tsv
-    plotphysio
-    rawmapper
-    skullstrip
-    slicereport
-spec2nii: https://github.com/wtclarke/spec2nii
 dcmtk: https://support.dcmtk.org/docs/pages.html
     dcmdump
     dump2dcm
@@ -36,21 +20,6 @@ heudiconv: https://heudiconv.readthedocs.io/en/latest/heuristics.html
 Bru2Nii: https://github.com/neurolabusc/Bru2Nii
 ```
 
-Example reorganizing DICOM data using BIDScoin:
-```
-dicomsort dicomfolder/sub-folder -r -e .IMA
-```
-
-Example converting dicom to BIDS using BIDScoin: 
-```
-Getting started:
-bidscoin -h
-
-Convert DICOM to BIDS:
-bidsmapper dicomfolder bidsoutputfolder
-bidscoiner dicomfolder bidsoutputfolder
-```
-
 Example converting Bruker data to Nifti
 ```
 Bru2 -o /Users/cr/dir2/out /Users/cr/dir/acqp

diff --git a/recipes/bidstools/build.sh b/recipes/bidstools/build.sh
@@ -3,7 +3,7 @@ set -e
 
 # this template file builds tools required for dicom conversion to bids
 export toolName='bidstools'
-export toolVersion='1.0.3'
+export toolVersion='1.0.4'
 # Don't forget to update version change in README.md!!!!!
 
 if [ "$1" != "" ]; then
@@ -23,20 +23,17 @@ neurodocker generate ${neurodocker_buildMode} \
    --miniconda version=latest \
                mamba=true \
                conda_install='python=3.10 traits=6.3.2' \
-               pip_install='bidscoin[spec2nii2bids,deface] heudiconv' \
-   --install opts="--quiet" wget zip qt6-base-dev libgl1 libgtk2.0-0 dcmtk xmedcon pigz libxcb-cursor0 \
+               pip_install='heudiconv' \
+   --install opts="--quiet" wget zip libgl1 libgtk2.0-0 dcmtk xmedcon pigz libxcb-cursor0 \
    --workdir /opt/bru2 \
    --run="wget https://github.com/neurolabusc/Bru2Nii/releases/download/v1.0.20180303/Bru2_Linux.zip" \
    --run="unzip Bru2_Linux.zip" \
    --dcm2niix method=source version=latest \
    --env PATH='$PATH':/opt/bru2 \
-   --env DEPLOY_BINS=bidscoin:bidscoiner:bidseditor:bidsmapper:bidsparticipants:deface:dicomsort:echocombine:medeface:physio2tsv:plotphysio:rawmapper:skullstrip:slicereport:dcm2niix:pydeface:spec2nii:Bru2:Bru2Nii:heudiconv \
+   --env DEPLOY_BINS=dcm2niix:Bru2:Bru2Nii:heudiconv \
    --copy README.md /README.md \
   > ${toolName}_${toolVersion}.Dockerfile
 
-   # requires yes | before neurodocker
-   # --fsl version=6.0.3 \ required for deface, but currently doesn't install because of problem with fsl conda environment
-
 
 if [ "$1" != "" ]; then
    ./../main_build.sh

diff --git a/recipes/bidstools/test.sh b/recipes/bidstools/test.sh
@@ -1,2 +0,0 @@
- export QT_DEBUG_PLUGINS=1
- bidseditor myproject/bids
Original file line number	Diff line number	Diff line change
		@@ -1,2 +0,0 @@
		export QT_DEBUG_PLUGINS=1
		bidseditor myproject/bids