From fd94a519fabec67ecf7e0187be0359dcf05fff5a Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Thu, 9 Jan 2025 17:44:36 +0100 Subject: [PATCH 1/4] Attempt targeting deeptools 4 --- recipes/deeptools/meta.yaml | 66 +++++++++++++++++++++++++++++++------ 1 file changed, 56 insertions(+), 10 deletions(-) diff --git a/recipes/deeptools/meta.yaml b/recipes/deeptools/meta.yaml index a6e95ba34a6cb..b64c45ecd1ab4 100644 --- a/recipes/deeptools/meta.yaml +++ b/recipes/deeptools/meta.yaml @@ -1,19 +1,41 @@ -{% set version = "3.5.5" %} + {% set version = "4.0.0" %} package: name: deeptools version: {{ version }} source: - url: https://github.com/deeptools/deepTools/archive/refs/tags/{{ version }}.tar.gz - sha256: f6dda39f552624758a9830cd4589ef43e7047284759b103cf833271cfa564dd1 + # url: https://github.com/deeptools/deepTools/archive/refs/tags/{{ version }}.tar.gz + # sha256: f6dda39f552624758a9830cd4589ef43e7047284759b103cf833271cfa564dd1 + git_url: https://github.com/deeptools/deepTools.git + git_rev: 010a1cfc1e7f57ae019e94083608dbd5e014e5f2 + sha256: ignored build: number: 0 - noarch: python run_exports: - {{ pin_subpackage("deeptools", max_pin="x") }} - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: | + set -xe + # export LANG=C.UTF-8 + # export LC_ALL=C.UTF-8 + export RUST_BACKTRACE=1 + export OPENSSL_NO_VENDOR=1 + export OPENSSL_DIR=$PREFIX + export OPENSSL_INCLUDE_DIR=$PREFIX/include + export OPENSSL_LIB_DIR=$PREFIX/lib + export CURL_STATIC_SSL=1 + export CURL_SYS_STATIC=1 + #export CARGO_NET_OFFLINE=true + export HTS_LIB_DIR=$PREFIX/lib + export HTS_INCLUDE_DIR=$PREFIX/include + export LIBCLANG_PATH=$PREFIX/lib # [linux] + # export CPLUS_INCLUDE_PATH=$PREFIX/include # [linux and aarch64] + export HTS_STATIC=1 + export HTS_SYS_BUNDLED=0 + cargo-bundle-licenses --format yaml --output RUST_THIRDPARTY.yml + maturin build -b pyo3 --interpreter "${PYTHON}" --release --strip + {{ PYTHON }} -m pip install ./target/wheels/*.whl --no-deps --no-build-isolation -vvv entry_points: - alignmentSieve = deeptools.alignmentSieve:main - bamCompare = deeptools.bamCompare:main @@ -37,15 +59,37 @@ build: - plotHeatmap = deeptools.plotHeatmap:main - plotPCA = deeptools.plotPCA:main - plotProfile = deeptools.plotProfile:main + - bamCoverage2 = deeptools.bamCoverage2:main + - bamCompare2 = deeptools.bamCompare2:main + - computeMatrix2 = deeptools.computeMatrix2:main requirements: + build: + - {{ compiler('c') }} + - {{ compiler('rust') }} + - make + - cargo-bundle-licenses host: - - python >=3.8 + - python <3.13 - pip + - maturin + - clangdev + - openssl + - curl + - htslib + - bzip2 + - xz + - zlib run: - - python >=3.8 - - pybigwig >=0.2.3 - - numpy >=1.9.0 + - {{ pin_compatible('openssl') }} + - {{ pin_compatible('curl') }} + - {{ pin_compatible('htslib') }} + - {{ pin_compatible('bzip2') }} + - {{ pin_compatible('xz') }} + - {{ pin_compatible('zlib') }} + - python + - pybigwig >=0.2.1 + - numpy >=2.0.0 - numpydoc >=0.5 - scipy >=0.17.0 - matplotlib-base >=3.5.0 @@ -65,7 +109,9 @@ about: home: https://github.com/deeptools/deepTools license: MIT license_family: MIT - license_file: LICENSE.txt + license_file: + - LICENSE.txt + - RUST_THIRDPARTY.yml summary: A set of user-friendly tools for normalization and visualzation of deep-sequencing data doc_url: https://deeptools.readthedocs.io/en/latest/ dev_url: https://github.com/deeptools/deepTools From 47b15c21791f9b4913dff7603a5488aa687e5b88 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Thu, 9 Jan 2025 18:00:02 +0100 Subject: [PATCH 2/4] Skip vcs_url linting --- recipes/deeptools/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/deeptools/meta.yaml b/recipes/deeptools/meta.yaml index b64c45ecd1ab4..010dfe5866bb2 100644 --- a/recipes/deeptools/meta.yaml +++ b/recipes/deeptools/meta.yaml @@ -140,3 +140,6 @@ extra: - usegalaxy-eu:deeptools_estimatereadfiltering - usegalaxy-eu:hicup_deduplicator - usegalaxy-eu:deeptools_bigwig_average + skip-lints: + - uses_vcs_url + From 41d834fb35ece97254fffc54b38557e75b1fc2d9 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 10 Jan 2025 11:46:15 +0100 Subject: [PATCH 3/4] Set deployment target for macos x86_64 builds --- recipes/deeptools/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/deeptools/meta.yaml b/recipes/deeptools/meta.yaml index 010dfe5866bb2..dc001789c5c70 100644 --- a/recipes/deeptools/meta.yaml +++ b/recipes/deeptools/meta.yaml @@ -33,6 +33,7 @@ build: # export CPLUS_INCLUDE_PATH=$PREFIX/include # [linux and aarch64] export HTS_STATIC=1 export HTS_SYS_BUNDLED=0 + export MACOSX_DEPLOYMENT_TARGET=13.0 # [osx and x86-64] cargo-bundle-licenses --format yaml --output RUST_THIRDPARTY.yml maturin build -b pyo3 --interpreter "${PYTHON}" --release --strip {{ PYTHON }} -m pip install ./target/wheels/*.whl --no-deps --no-build-isolation -vvv From e771ea8a69b646b7d54e652d49934352c6ead867 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 10 Jan 2025 13:03:11 +0100 Subject: [PATCH 4/4] Update recipes/deeptools/meta.yaml --- recipes/deeptools/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/deeptools/meta.yaml b/recipes/deeptools/meta.yaml index dc001789c5c70..efbe8d0301821 100644 --- a/recipes/deeptools/meta.yaml +++ b/recipes/deeptools/meta.yaml @@ -71,7 +71,7 @@ requirements: - make - cargo-bundle-licenses host: - - python <3.13 + - python - pip - maturin - clangdev