fix: prepend system libraries to LD_LIBRARY_PATH

The libraries for Matlab compiler runtime 2010a are being found before the system libraries, and flameo was linking to one of matlab's libraries. This commit prepends the system libraries to LD_LIBRARY_PATH so that flameo (and other binaries) do not link to Matlab's libraries.

Author: Jakub Kaczmarzyk

docker/generate_dockerfiles.sh

@@ -66,6 +66,7 @@ function generate_base_dockerfile() {
     --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \
     --label maintainer="The nipype developers https://github.com/nipy/nipype" \
     --spm12 version=r7219 \
+    --env 'LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
     --freesurfer version=6.0.0-min \
     --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tCjUxNzIKICpDdnVtdkVWM3pUZmcKRlM1Si8yYzFhZ2c0RQoiID4gL29wdC9mcmVlc3VyZmVyLTYuMC4wLW1pbi9saWNlbnNlLnR4dA==" | base64 -d | sh' \
     --install afni ants apt-utils bzip2 convert3d file fsl-core \