Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FIX: Include dwidenoise within docker image #1196

Merged
merged 1 commit into from
Mar 19, 2024
Merged

Conversation

oesteban
Copy link
Member

@oesteban oesteban commented Mar 19, 2024

Implements @effigies' solution leveraging Docker multi-staged builds.

Checked linked libraries within the Docker container:

$ ldd /usr/local/bin/dwidenoise
	linux-vdso.so.1 (0x00007fff6db65000)
	libmrtrix.so => /usr/local/bin/../lib/libmrtrix.so (0x00007f4e2b757000)
	libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f4e2b574000)
	libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f4e2b48d000)
	libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f4e2b472000)
	libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4e2b46d000)
	libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f4e2b242000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f4e2bac2000)
	libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f4e2b227000)
	libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f4e2b19f000)
	libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f4e2b162000)
	librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f4e2b15d000)
	libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f4e2b0bb000)
	libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f4e2afa7000)
	liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f4e2af7e000)
	libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f4e2af6d000)
	libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f4e2ae87000)
	libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f4e2ae71000)
	libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f4e2ae65000)

ldd /usr/local/lib/libmrtrix.so
	linux-vdso.so.1 (0x00007ffc0a0b6000)
	libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f431b203000)
	libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f431b17b000)
	libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f431b13e000)
	libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f431af5b000)
	libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f431ae74000)
	libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f431ae57000)
	libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f431ae52000)
	libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f431ac29000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f431b4d5000)
	libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f431ab89000)
	libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f431aa75000)
	liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f431aa4c000)
	libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f431aa39000)
	libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f431a953000)
	libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f431a93d000)
	librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f431a938000)
	libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f431a92e000)

And also tested MRIQC locally on DWI data.

Resolves: #1175.

Implements [@effigies'
solution](#1175 (comment))
leveraging Docker multi-staged builds.

Checked linked libraries within the Docker container:

```
$ ldd /usr/local/bin/dwidenoise
	linux-vdso.so.1 (0x00007fff6db65000)
	libmrtrix.so => /usr/local/bin/../lib/libmrtrix.so (0x00007f4e2b757000)
	libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f4e2b574000)
	libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f4e2b48d000)
	libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f4e2b472000)
	libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4e2b46d000)
	libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f4e2b242000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f4e2bac2000)
	libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f4e2b227000)
	libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f4e2b19f000)
	libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f4e2b162000)
	librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f4e2b15d000)
	libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f4e2b0bb000)
	libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f4e2afa7000)
	liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f4e2af7e000)
	libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f4e2af6d000)
	libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f4e2ae87000)
	libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f4e2ae71000)
	libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f4e2ae65000)

ldd /usr/local/lib/libmrtrix.so
	linux-vdso.so.1 (0x00007ffc0a0b6000)
	libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f431b203000)
	libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f431b17b000)
	libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f431b13e000)
	libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f431af5b000)
	libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f431ae74000)
	libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f431ae57000)
	libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f431ae52000)
	libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f431ac29000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f431b4d5000)
	libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f431ab89000)
	libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f431aa75000)
	liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f431aa4c000)
	libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f431aa39000)
	libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f431a953000)
	libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f431a93d000)
	librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f431a938000)
	libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f431a92e000)
```

And also tested *MRIQC* locally on DWI data.

Resolves: #1175.
@oesteban oesteban merged commit 48a8154 into master Mar 19, 2024
10 of 11 checks passed
@oesteban oesteban deleted the fix/dwidenoise-missing branch March 19, 2024 12:58
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

The Dockerfile is missing installation of dwidenoise from Mrtrix3 to run the dwi workflow
1 participant