diff --git a/recipes/snapatac2/build.sh b/recipes/snapatac2/build.sh index e2ff247a81a4f..3f270cc862d95 100644 --- a/recipes/snapatac2/build.sh +++ b/recipes/snapatac2/build.sh @@ -1,11 +1,5 @@ #!/bin/bash -ex -# Use a custom temporary directory as home on macOS. -# (not sure why this is useful, but people use it in bioconda recipes) -if [ `uname` == Darwin ]; then - export HOME=`mktemp -d` -fi - # build statically linked binary with Rust RUST_BACKTRACE=1 # Build the package using maturin - should produce *.whl files. diff --git a/recipes/snapatac2/build_failure.linux-64.yaml b/recipes/snapatac2/build_failure.linux-64.yaml deleted file mode 100644 index 192d0da24c090..0000000000000 --- a/recipes/snapatac2/build_failure.linux-64.yaml +++ /dev/null @@ -1,4 +0,0 @@ -recipe_sha: 0020e1f18882dacb116e05fb00a1e435b21713b2e0a803ece479d299f8c00347 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: disk space -reason: GitHub Actions runs out of space trying to build all python versions. \ No newline at end of file diff --git a/recipes/snapatac2/build_failure.osx-64.yaml b/recipes/snapatac2/build_failure.osx-64.yaml deleted file mode 100644 index 4a6f367e00bb0..0000000000000 --- a/recipes/snapatac2/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 0020e1f18882dacb116e05fb00a1e435b21713b2e0a803ece479d299f8c00347 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - = note: ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libproc_macro-d9904b6b430ac650.rlib(proc_macro-d9904b6b430ac650.proc_macro.f7284eae513ccf25-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib(core-1638dc700d175798.core.b1c2fc210f4dfff9-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib(alloc-0ff05b9b25b786cc.alloc.9242d371e396bc4c-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib(hashbrown-0e3ea0ec18336be2.hashbrown.febebf65344cb99d-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib(rustc_demangle-37f4c48e230f618e.rustc_demangle.9fdffeb2b56169d1-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib(gimli-de95e5c2a2ace281.gimli.72653df79598dcb2-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib(object-0e1339b212cc7409.object.e3756fe3fb577255-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib(memchr-925e672b3deb429c.memchr.4dc4a05d80618598-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib(addr2line-e92d517a950bccd8.addr2line.7eb29e6a0a38fefd-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib(panic_unwind-8ce93eee8bf4c86e.panic_unwind.a3b8ea81b157ee45-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib(compiler_builtins-7f42af62722c8f43.compiler_builtins.19fed66cffb9e9f5-cgu.089.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - Undefined symbols for architecture x86_64: - "_getentropy", referenced from: - std::sys::pal::unix::rand::hashmap_random_keys::hcc27ed0e9fd421d6 in libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o) - ld: symbol(s) not found for architecture x86_64 - clang-16: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: could not compile serde_derive (lib) due to 1 previous error - maturin failed - Caused by: Failed to build a native library through cargo - Caused by: Cargo build finished with "exit status: 101": env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.11-64bit" PYO3_PYTHON="/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python" PYTHON_SYS_EXECUTABLE="/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python" "cargo" "rustc" "--features" "pyo3/extension-module" "--target" "x86_64-apple-darwin" "--message-format" "json-render-diagnostics" "--manifest-path" "/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work/snapatac2-python/Cargo.toml" "--release" "--lib" "--" "-C" "link-arg=-undefined" "-C" "link-arg=dynamic_lookup" "-C" "link-args=-Wl,-install_name,@rpath/snapatac2._snapatac2.cpython-311-darwin.so" "-C" "link-arg=-s" - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/snapatac2/cargo.toml.patch - Traceback (most recent call last): - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/snapatac2/cargo.toml.patch with args: - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - ['-Np1', '-i', '/tmp/tmpdjpsa4y_/cargo.toml.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ cargo.toml.patch ]] - - Key: - - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/snapatac2-2.6.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work/conda_build.sh']' returned non-zero exit status 1. - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/snapatac2-2.6.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 -# Last 100 lines of the build log. diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml index 8989a9d16459f..ace1bae3532d1 100644 --- a/recipes/snapatac2/meta.yaml +++ b/recipes/snapatac2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "snapatac2" %} -{% set version = "2.6.4" %} -{% set sha256 = "6ce80ae2c67f0ae05efed2b785b25e4d13fcc9d58697291b7d578a628b74bd05" %} +{% set version = "2.7.0" %} +{% set sha256 = "a37e86001da1e8f812d2e2dfda157ce131b8a0b54a44ae5bd72733c0171d4f1d" %} package: name: {{ name }} @@ -11,9 +11,10 @@ source: sha256: {{ sha256 }} patches: - cargo.toml.patch + - pyproject.toml.patch build: - number: 1 + number: 0 skip: True # [py < 39 or py > 312] run_exports: - {{ pin_subpackage('snapatac2', max_pin="x") }} @@ -32,44 +33,42 @@ requirements: run: - python - anndata - - harmonypy >=0.0.9 - python-igraph >=0.10.3 - multiprocess - macs3 - natsort - numpy >=1.16.0 - pandas >=1.0,<2.1.2 - - plotly >=5.6.0 - - polars >=0.20.0 + - plotly >=5.19.0 + - polars >=1.0 - pooch >=1.6.0 - pyarrow - pyfaidx >=0.7.0,<0.8.0 - python-kaleido - rustworkx - - scanorama >=1.7.3 - - scanpy - scipy >=1.4 - scikit-learn >=1.0 - - scvi-tools >=1.0 - tqdm >=4.62 - typing_extensions - - umap-learn >=0.5.0 - - xgboost >=1.4 test: imports: - snapatac2 about: - home: https://github.com/kaizhang/SnapATAC2 - summary: "SnapATAC2: Single-cell epigenomics analysis pipeline" + home: "https://github.com/kaizhang/SnapATAC2" + summary: "SnapATAC2: Single-cell epigenomics analysis pipeline." license: MIT license_family: MIT license_file: LICENSE - doc_url: https://kzhang.org/SnapATAC2/ - dev_url: https://github.com/kaizhang/SnapATAC2 + doc_url: "https://kzhang.org/SnapATAC2" + dev_url: "https://github.com/kaizhang/SnapATAC2" extra: identifiers: - biotools:snapatac - doi:10.1038/s41592-023-02139-9 + - usegalaxy-eu:snapatac2_preprocessing + - usegalaxy-eu:snapatac2_clustering + - usegalaxy-eu:snapatac2_peaks_and_motif + - usegalaxy-eu:snapatac2_plotting diff --git a/recipes/snapatac2/pyproject.toml.patch b/recipes/snapatac2/pyproject.toml.patch new file mode 100644 index 0000000000000..1c87870e9049d --- /dev/null +++ b/recipes/snapatac2/pyproject.toml.patch @@ -0,0 +1,14 @@ +diff --git a/pyproject.toml b/pyproject.toml +index 0cc0ca0..eeb5899 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -7,6 +7,9 @@ features = ["pyo3/extension-module"] + python-source = "python" + module-name = "snapatac2._snapatac2" + manifest-path = "snapatac2-python/Cargo.toml" ++strip = true ++profile = "release" ++locked = true + + [project] + name = "snapatac2"