downgrade to version 6.0.1

bids-apps · Jan 8, 2023 · 6e49c76 · 6e49c76
1 parent f1742ff
commit 6e49c76
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Showing 2 changed files with 18 additions and 14 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,12 +1,12 @@
 # Generated by Neurodocker and Reproenv.
 
 FROM bids/base_validator
-ENV FSLDIR="/opt/fsl-6.0.3" \
-    PATH="/opt/fsl-6.0.3/bin:$PATH" \
+ENV FSLDIR="/opt/fsl-6.0.1" \
+    PATH="/opt/fsl-6.0.1/bin:$PATH" \
     FSLOUTPUTTYPE="NIFTI_GZ" \
     FSLMULTIFILEQUIT="TRUE" \
-    FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
-    FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
+    FSLTCLSH="/opt/fsl-6.0.1/bin/fsltclsh" \
+    FSLWISH="/opt/fsl-6.0.1/bin/fslwish" \
     FSLLOCKDIR="" \
     FSLMACHINELIST="" \
     FSLREMOTECALL="" \
@@ -37,11 +37,15 @@ RUN apt-get update -qq \
            wget \
     && rm -rf /var/lib/apt/lists/* \
     && echo "Downloading FSL ..." \
-    && mkdir -p /opt/fsl-6.0.3 \
-    && curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
-    | tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
+    && mkdir -p /opt/fsl-6.0.1 \
+    && curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos6_64.tar.gz \
+    | tar -xz -C /opt/fsl-6.0.1 --strip-components 1 \
     && echo "Installing FSL conda environment ..." \
-    && bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3
+    && bash /opt/fsl-6.0.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.1 \
+    && echo "Downgrading deprecation module per https://github.com/kaczmarj/neurodocker/issues/271#issuecomment-514523420" \
+    && /opt/fsl-6.0.1/fslpython/bin/conda install -n fslpython -c conda-forge -y deprecation==1.* \
+    && echo "Removing bundled with FSLeyes libz likely incompatible with the one from OS" \
+    && rm -f /opt/fsl-6.0.1/bin/FSLeyes/libz.so.1
 
 # Save specification to JSON.
 RUN printf '{ \
@@ -59,12 +63,12 @@ RUN printf '{ \
     { \
       "name": "env", \
       "kwds": { \
-        "FSLDIR": "/opt/fsl-6.0.3", \
-        "PATH": "/opt/fsl-6.0.3/bin:$PATH", \
+        "FSLDIR": "/opt/fsl-6.0.1", \
+        "PATH": "/opt/fsl-6.0.1/bin:$PATH", \
         "FSLOUTPUTTYPE": "NIFTI_GZ", \
         "FSLMULTIFILEQUIT": "TRUE", \
-        "FSLTCLSH": "/opt/fsl-6.0.3/bin/fsltclsh", \
-        "FSLWISH": "/opt/fsl-6.0.3/bin/fslwish", \
+        "FSLTCLSH": "/opt/fsl-6.0.1/bin/fsltclsh", \
+        "FSLWISH": "/opt/fsl-6.0.1/bin/fslwish", \
         "FSLLOCKDIR": "", \
         "FSLMACHINELIST": "", \
         "FSLREMOTECALL": "", \
@@ -74,7 +78,7 @@ RUN printf '{ \
     { \
       "name": "run", \
       "kwds": { \
-        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bc \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    dc \\\\\\n    file \\\\\\n    libfontconfig1 \\\\\\n    libfreetype6 \\\\\\n    libgl1-mesa-dev \\\\\\n    libgl1-mesa-dri \\\\\\n    libglu1-mesa-dev \\\\\\n    libgomp1 \\\\\\n    libice6 \\\\\\n    libopenblas-base \\\\\\n    libxcursor1 \\\\\\n    libxft2 \\\\\\n    libxinerama1 \\\\\\n    libxrandr2 \\\\\\n    libxrender1 \\\\\\n    libxt6 \\\\\\n    nano \\\\\\n    sudo \\\\\\n    wget\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FSL ...\\"\\nmkdir -p /opt/fsl-6.0.3\\ncurl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \\\\\\n| tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \\necho \\"Installing FSL conda environment ...\\"\\nbash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3" \
+        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bc \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    dc \\\\\\n    file \\\\\\n    libfontconfig1 \\\\\\n    libfreetype6 \\\\\\n    libgl1-mesa-dev \\\\\\n    libgl1-mesa-dri \\\\\\n    libglu1-mesa-dev \\\\\\n    libgomp1 \\\\\\n    libice6 \\\\\\n    libopenblas-base \\\\\\n    libxcursor1 \\\\\\n    libxft2 \\\\\\n    libxinerama1 \\\\\\n    libxrandr2 \\\\\\n    libxrender1 \\\\\\n    libxt6 \\\\\\n    nano \\\\\\n    sudo \\\\\\n    wget\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FSL ...\\"\\nmkdir -p /opt/fsl-6.0.1\\ncurl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos6_64.tar.gz \\\\\\n| tar -xz -C /opt/fsl-6.0.1 --strip-components 1 \\necho \\"Installing FSL conda environment ...\\"\\nbash /opt/fsl-6.0.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.1\\necho \\"Downgrading deprecation module per https://github.com/kaczmarj/neurodocker/issues/271#issuecomment-514523420\\"\\n/opt/fsl-6.0.1/fslpython/bin/conda install -n fslpython -c conda-forge -y deprecation==1.*\\necho \\"Removing bundled with FSLeyes libz likely incompatible with the one from OS\\"\\nrm -f /opt/fsl-6.0.1/bin/FSLeyes/libz.so.1" \
       } \
     } \
   ] \

diff --git a/Makefile b/Makefile
@@ -6,4 +6,4 @@ Dockerfile:
 			--base-image bids/base_validator \
 			--pkg-manager apt \
 			--yes \
-			--fsl method=binaries version=6.0.3 > Dockerfile
+			--fsl method=binaries version=6.0.1 > Dockerfile