From 84796e97f3cd9156c385cf01413bb5869feccd4f Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 21:56:46 +1000 Subject: [PATCH 01/13] add lrge v0.1.0 --- recipes/lrge/meta.yaml | 44 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/lrge/meta.yaml diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml new file mode 100644 index 0000000000000..ac42e7dd1a378 --- /dev/null +++ b/recipes/lrge/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "0.1.0" %} +{% set name = "lrge" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/mbhall88/{{ name }}/archive/{{ name }}-{{ version }}.tar.gz + sha256: 817afa20b838fbdd8de35a815567ffd8f2b63486d97e1d67e16182235a474692 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('lrge', max_pin="x.x") }} + script: + - cargo-bundle-licenses --format yaml --output THIRDPARTY.yml + - cargo install -v --locked --no-track --root $PREFIX --path . + +requirements: + build: + - {{ compiler('rust') }} + - cargo-bundle-licenses + - {{ compiler('c') }} + - {{ stdlib('libc') }} + +test: + commands: + - lrge --version + +about: + home: https://github.com/mbhall88/lrge + license: MIT + license_file: + - LICENSE + - THIRDPARTY.yml # this file is generated by cargo-bundle-licenses + summary: Genome size estimation from long read overlaps + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - mbhall88 \ No newline at end of file From 8634fa7b2de3d48f377fbbe233be4c1c241ee19a Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 22:17:08 +1000 Subject: [PATCH 02/13] fix incorrect usage of stdlib --- recipes/lrge/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index ac42e7dd1a378..fa8e8136da941 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -22,7 +22,7 @@ requirements: - {{ compiler('rust') }} - cargo-bundle-licenses - {{ compiler('c') }} - - {{ stdlib('libc') }} + - {{ stdlib('c') }} test: commands: From 216541242a15d364a98ead9819e002a210d9fdbf Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 22:23:19 +1000 Subject: [PATCH 03/13] remove comment --- recipes/lrge/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index fa8e8136da941..8ce19e5323f99 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -33,7 +33,7 @@ about: license: MIT license_file: - LICENSE - - THIRDPARTY.yml # this file is generated by cargo-bundle-licenses + - THIRDPARTY.yml summary: Genome size estimation from long read overlaps extra: From d717ce6bb0dffe6d3bfc2d87f72cb753d26c639c Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 22:35:49 +1000 Subject: [PATCH 04/13] skip whitespace lint --- recipes/lrge/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 8ce19e5323f99..79d6118934df3 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -37,6 +37,8 @@ about: summary: Genome size estimation from long read overlaps extra: + skip-lints: + - version_constraints_missing_whitespace # see https://github.com/bioconda/bioconda-recipes/issues/51185 additional-platforms: - linux-aarch64 - osx-arm64 From 6587f095619fac30df83d0083611827a813bc8a5 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 22:50:55 +1000 Subject: [PATCH 05/13] specify package to install --- recipes/lrge/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 79d6118934df3..06c092125293d 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -15,7 +15,7 @@ build: - {{ pin_subpackage('lrge', max_pin="x.x") }} script: - cargo-bundle-licenses --format yaml --output THIRDPARTY.yml - - cargo install -v --locked --no-track --root $PREFIX --path . + - cargo install -v --locked --no-track --root $PREFIX --path . -p {{ name }} requirements: build: From 3dc57802b1d153b4e266e7722fdf4a5cf35e882a Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 23:15:25 +1000 Subject: [PATCH 06/13] specify bin instead of package --- recipes/lrge/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 06c092125293d..7b85f8137a5b8 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -15,7 +15,7 @@ build: - {{ pin_subpackage('lrge', max_pin="x.x") }} script: - cargo-bundle-licenses --format yaml --output THIRDPARTY.yml - - cargo install -v --locked --no-track --root $PREFIX --path . -p {{ name }} + - cargo install -v --locked --no-track --root $PREFIX --path . --bin {{ name }} requirements: build: From 91955f1c27969d55f240f63e954838ed221780b5 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 23:38:22 +1000 Subject: [PATCH 07/13] specify path to bin crate --- recipes/lrge/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 7b85f8137a5b8..cdd2382c1fb5f 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -15,7 +15,7 @@ build: - {{ pin_subpackage('lrge', max_pin="x.x") }} script: - cargo-bundle-licenses --format yaml --output THIRDPARTY.yml - - cargo install -v --locked --no-track --root $PREFIX --path . --bin {{ name }} + - cargo install -v --locked --no-track --root $PREFIX --path lrge requirements: build: From ae3c48bc73c8d7ec67233f636d939eab6c0f352b Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 25 Nov 2024 23:57:45 +1000 Subject: [PATCH 08/13] add zlib to requirements --- recipes/lrge/meta.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index cdd2382c1fb5f..33bc2228da0be 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -23,6 +23,11 @@ requirements: - cargo-bundle-licenses - {{ compiler('c') }} - {{ stdlib('c') }} + - zlib + host: + - zlib + run: + - zlib test: commands: From 2d2ba68ebcdb4fd22c23612269249a7358eccd61 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Tue, 26 Nov 2024 11:06:46 +1000 Subject: [PATCH 09/13] update to 0.1.1 --- recipes/lrge/meta.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 33bc2228da0be..0795312f20cac 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} {% set name = "lrge" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ name }}-{{ version }}.tar.gz - sha256: 817afa20b838fbdd8de35a815567ffd8f2b63486d97e1d67e16182235a474692 + sha256: 768b26435c8afa3eda00889818937276a0f0b0b8a2f0e3e17d67f183915c3da2 build: number: 0 @@ -26,8 +26,6 @@ requirements: - zlib host: - zlib - run: - - zlib test: commands: From 47ed4d21ae8dccf0792a29637ed1d66f4c5be2a6 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Tue, 26 Nov 2024 11:49:52 +1000 Subject: [PATCH 10/13] move to build script and set CFLAGS --- recipes/lrge/build.sh | 10 ++++++++++ recipes/lrge/meta.yaml | 3 --- 2 files changed, 10 insertions(+), 3 deletions(-) create mode 100644 recipes/lrge/build.sh diff --git a/recipes/lrge/build.sh b/recipes/lrge/build.sh new file mode 100644 index 0000000000000..1ad01b132a45e --- /dev/null +++ b/recipes/lrge/build.sh @@ -0,0 +1,10 @@ +#!/usr/bin/env bash + +set -euo pipefail + +export CFLAGS="${CFLAGS} -fcommon" +export CXXFLAGS="${CFLAGS} -fcommon" + +cargo-bundle-licenses --format yaml --output THIRDPARTY.yml + +RUST_BACKTRACE=full cargo install -v --locked --no-track --root "$PREFIX" --path lrge \ No newline at end of file diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 0795312f20cac..98d2914fcc4e4 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -13,9 +13,6 @@ build: number: 0 run_exports: - {{ pin_subpackage('lrge', max_pin="x.x") }} - script: - - cargo-bundle-licenses --format yaml --output THIRDPARTY.yml - - cargo install -v --locked --no-track --root $PREFIX --path lrge requirements: build: From 0efd0c2f5cfef6570f6befc1ea93743e44b4429c Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Tue, 26 Nov 2024 12:57:27 +1000 Subject: [PATCH 11/13] try bindgen flags --- recipes/lrge/build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lrge/build.sh b/recipes/lrge/build.sh index 1ad01b132a45e..5c534894a8721 100644 --- a/recipes/lrge/build.sh +++ b/recipes/lrge/build.sh @@ -2,8 +2,8 @@ set -euo pipefail -export CFLAGS="${CFLAGS} -fcommon" -export CXXFLAGS="${CFLAGS} -fcommon" +# Make sure bindgen passes on our compiler flags. +export BINDGEN_EXTRA_CLANG_ARGS="${CPPFLAGS} ${CFLAGS} ${LDFLAGS}" cargo-bundle-licenses --format yaml --output THIRDPARTY.yml From 42339a832f1dd53f017a3570ad5ea08ae2d2e8f3 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Tue, 26 Nov 2024 13:30:10 +1000 Subject: [PATCH 12/13] try rustflags --- recipes/lrge/build.sh | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/recipes/lrge/build.sh b/recipes/lrge/build.sh index 5c534894a8721..fb44d1e964449 100644 --- a/recipes/lrge/build.sh +++ b/recipes/lrge/build.sh @@ -2,9 +2,6 @@ set -euo pipefail -# Make sure bindgen passes on our compiler flags. -export BINDGEN_EXTRA_CLANG_ARGS="${CPPFLAGS} ${CFLAGS} ${LDFLAGS}" - cargo-bundle-licenses --format yaml --output THIRDPARTY.yml -RUST_BACKTRACE=full cargo install -v --locked --no-track --root "$PREFIX" --path lrge \ No newline at end of file +RUST_BACKTRACE=full RUSTFLAGS="-C linker=$CC" cargo install -v --locked --no-track --root "$PREFIX" --path lrge \ No newline at end of file From ca0322d4e6d15baad64add6c1b9ae5c8d22e2cab Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Tue, 26 Nov 2024 14:25:29 +1000 Subject: [PATCH 13/13] add clangdev --- recipes/lrge/build.sh | 5 +++++ recipes/lrge/meta.yaml | 1 + 2 files changed, 6 insertions(+) diff --git a/recipes/lrge/build.sh b/recipes/lrge/build.sh index fb44d1e964449..d40cec8b788d8 100644 --- a/recipes/lrge/build.sh +++ b/recipes/lrge/build.sh @@ -2,6 +2,11 @@ set -euo pipefail +export INCLUDE_PATH="${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -fcommon" +export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include" + cargo-bundle-licenses --format yaml --output THIRDPARTY.yml RUST_BACKTRACE=full RUSTFLAGS="-C linker=$CC" cargo install -v --locked --no-track --root "$PREFIX" --path lrge \ No newline at end of file diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 98d2914fcc4e4..944cba96b00a9 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -23,6 +23,7 @@ requirements: - zlib host: - zlib + - clangdev test: commands: