Add recipe for mrtrix3 (#53168)

* Add recipe for mrtrix3 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add dummy test command Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update recipes/mrtrix3/meta.yaml * Pass CXX as an env var to ./configure Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try with temporary symlinks for gcc and g++ that are foundable in PATH Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Move cdt(...) requirements to `build:` Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Use `ARCH=native` because otherwise it uses `aarch64` for ARM64 and breaks Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Move all requirements from host to build Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add host dependency to libxcb ``` 13:50:54 BIOCONDA INFO (OUT) $BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libxcb.so.1, needed by $BUILD_PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/../lib/libX11.so.6, not found (try using -rpath or -rpath-link) ``` Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add host dependency to xcb-util-renderutil too Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Move xsb requirements to `build`, next to all other X requirements Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try by moving all `host` reqs to `build` Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * eigen needs to be in `host` to be findable Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Debug libxcb Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add libxcb for all requirements Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try finding libxcb with -rpath Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Export RPATH too Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try with RPATH looking in BUILD_PREFIX Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try with full path to libxcb.so.1 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try without full path to libxcb.so/dylib. Leave only -lxcb Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Disable the build for OSX due to new kind of issues with libxcb Add a test command Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
bioconda · Jan 15, 2025 · ba4539e · ba4539e
1 parent 7523d4f
commit ba4539e
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diff --git a/recipes/mrtrix3/build.sh b/recipes/mrtrix3/build.sh
@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+set -x
+
+export RPATH="${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -idirafter ${PREFIX}/include" 
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -lxcb"
+export LINKFLAGS="-L${PREFIX}/lib -lxcb"
+export LINKLIB_FLAGS="${LINKFLAGS}"
+export EIGEN_CFLAGS="-idirafter ${PREFIX}/include/eigen3"
+
+mkdir -p "${PREFIX}"/{bin,lib,share}
+
+ln -s ${CC} ${CONDA_PREFIX}/bin/gcc
+ln -s ${CXX} ${CONDA_PREFIX}/bin/g++
+
+ARCH=native CFLAGS="${CXXFLAGS}" ./configure -conda -openmp || (cat configure.log && exit 123)
+
+./build 
+
+cp -r bin lib share "${PREFIX}"
+
+unlink ${CONDA_PREFIX}/bin/g++
+unlink ${CONDA_PREFIX}/bin/gcc
diff --git a/recipes/mrtrix3/meta.yaml b/recipes/mrtrix3/meta.yaml
@@ -0,0 +1,70 @@
+{% set name = "mrtrix3" %}
+{% set version = "3.0.4" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/MRtrix3/mrtrix3/archive/refs/tags/{{ version }}.tar.gz
+  sha256: f1d1aa289cfc3e46e3a8eca93594b23d061c6d50a0cd03727433a7e2cd14f71a
+
+build:
+  skip: True  # [osx]
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - pkg-config
+    - {{ cdt('xorg-x11-proto-devel') }}  # [linux]
+    - {{ cdt('libx11-devel') }}          # [linux]
+    - {{ cdt('libxext-devel') }}         # [linux]
+    - {{ cdt('libxrender-devel') }}      # [linux]
+    - {{ cdt('mesa-libgl-devel') }}      # [linux]
+    - {{ cdt('mesa-libegl-devel') }}     # [linux]
+    - {{ cdt('mesa-dri-drivers') }}      # [linux]
+    - {{ cdt('libxau-devel') }}          # [linux]
+    - {{ cdt('libselinux-devel') }}      # [linux]
+    - {{ cdt('libxdamage') }}            # [linux]
+    - {{ cdt('libxdamage-devel') }}      # [linux]
+    - {{ cdt('libxfixes') }}             # [linux]
+    - {{ cdt('libxfixes-devel') }}       # [linux]
+    - {{ cdt('libxxf86vm') }}            # [linux]
+    - {{ cdt('libxxf86vm-devel') }}      # [linux]
+    - qt >=5.15
+    - python
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+  host:
+    - eigen >=3.2
+    - libtiff >=4.0
+    - zlib
+    - fftw >=3.0
+    - libxcb
+  run:
+    - qt >=5.15
+    - zlib 
+    - libtiff >=4.0
+    - fftw >=3.0
+
+test:
+  commands:
+    - mrconvert --help
+
+about:
+  home: https://www.mrtrix.org
+  license: MPL-2.0
+  license_family: MOZILLA
+  license_file: LICENCE.txt
+  summary: A set of tools to perform various advanced diffusion MRI analyses, 
+    including constrained spherical deconvolution (CSD), probabilistic tractography, 
+    track-density imaging, and apparent fibre density
+  dev_url: https://github.com/MRtrix3/mrtrix3
+  doc_url: https://www.mrtrix.org/documentation/
+
+extra:
+  additional-platforms:
+    - linux-aarch64