From d6b2f35087b22b61a0851584fc61e98ac1ed8ede Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 12:50:10 -0500 Subject: [PATCH 1/4] enh: Add rna-seqc python utilities and qtl package Using PyPI skeleton recipes. --- recipes/qtl/meta.yaml | 46 +++++++++++++++++++++++++++++++ recipes/rna-seqc-python/meta.yaml | 46 +++++++++++++++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 recipes/qtl/meta.yaml create mode 100644 recipes/rna-seqc-python/meta.yaml diff --git a/recipes/qtl/meta.yaml b/recipes/qtl/meta.yaml new file mode 100644 index 0000000000000..2617dd49850f7 --- /dev/null +++ b/recipes/qtl/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "qtl" %} +{% set version = "0.1.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/qtl-{{ version }}.tar.gz + sha256: 8fdb99cda1ceff578a233db6c15a944fa57b43a2826af41c292e36848906117b + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python + - pip + run: + - python + - numpy + - pandas + - scipy + - matplotlib-base + - seaborn + - pybigwig + - bx-python + +test: + imports: + - qtl + commands: + - pip check + requires: + - pip + +about: + summary: Utilities for analyzing and visualizing QTL data + license: BSD-3-Clause + license_file: LICENSE + +extra: + recipe-maintainers: + - lrvdijk diff --git a/recipes/rna-seqc-python/meta.yaml b/recipes/rna-seqc-python/meta.yaml new file mode 100644 index 0000000000000..1600c208f31a6 --- /dev/null +++ b/recipes/rna-seqc-python/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "rnaseqc" %} +{% set version = "0.0.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/rnaseqc-{{ version }}.tar.gz + sha256: 857ad1ad54f2b563163d75ff8c5f2439208d06980b7c8ded279bd59d19c48a0f + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python + - pip + run: + - python + - numpy + - pandas + - matplotlib-base + - seaborn + - qtl + - agutil + - nbformat + +test: + imports: + - rnaseqc + commands: + - pip check + requires: + - pip + +about: + summary: Multi-sample visualization of metrics from RNA-SeQC + license: '' + license_file: PLEASE_ADD_LICENSE_FILE + +extra: + recipe-maintainers: + - lrvdijk From 324d35fcc0cb7c326096c28d2f243dc4a8d526fd Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 13:07:25 -0500 Subject: [PATCH 2/4] fix: Include home, license and run_exports --- recipes/qtl/meta.yaml | 3 +++ recipes/rna-seqc-python/meta.yaml | 12 +++++++----- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/qtl/meta.yaml b/recipes/qtl/meta.yaml index 2617dd49850f7..72b93e4a3b14e 100644 --- a/recipes/qtl/meta.yaml +++ b/recipes/qtl/meta.yaml @@ -13,6 +13,8 @@ build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 + run_exports: + - {{ pin_subpackage("rna-seqc-python", max_pin="x.x") }} requirements: host: @@ -37,6 +39,7 @@ test: - pip about: + home: https://github.com/broadinstitute/pyqtl summary: Utilities for analyzing and visualizing QTL data license: BSD-3-Clause license_file: LICENSE diff --git a/recipes/rna-seqc-python/meta.yaml b/recipes/rna-seqc-python/meta.yaml index 1600c208f31a6..c0cfabfddca36 100644 --- a/recipes/rna-seqc-python/meta.yaml +++ b/recipes/rna-seqc-python/meta.yaml @@ -1,8 +1,8 @@ -{% set name = "rnaseqc" %} +{% set pypi_name = "rnaseqc" %} {% set version = "0.0.3" %} package: - name: {{ name|lower }} + name: "rna-seqc-python" version: {{ version }} source: @@ -13,6 +13,8 @@ build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 + run_exports: + - {{ pin_subpackage("rna-seqc-python", max_pin="x.x") }} requirements: host: @@ -25,7 +27,6 @@ requirements: - matplotlib-base - seaborn - qtl - - agutil - nbformat test: @@ -37,9 +38,10 @@ test: - pip about: + home: https://github.com/broadinstitute/rnaseqc summary: Multi-sample visualization of metrics from RNA-SeQC - license: '' - license_file: PLEASE_ADD_LICENSE_FILE + license: BSD 3-clause + license_family: BSD extra: recipe-maintainers: From 01655f177f8160072e927e95ac1b2dff80ad692b Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 13:26:25 -0500 Subject: [PATCH 3/4] fix: Fix incorrect package name in qtl --- recipes/qtl/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/qtl/meta.yaml b/recipes/qtl/meta.yaml index 72b93e4a3b14e..84c3522f35ee4 100644 --- a/recipes/qtl/meta.yaml +++ b/recipes/qtl/meta.yaml @@ -14,7 +14,7 @@ build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 run_exports: - - {{ pin_subpackage("rna-seqc-python", max_pin="x.x") }} + - {{ pin_subpackage("qtl", max_pin="x.x") }} requirements: host: From 624351d9a6650acb9b75b9b247064a3aeae7a67e Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 11 Oct 2024 13:48:02 -0500 Subject: [PATCH 4/4] fix: Template variable name in rna-seqc-python --- recipes/rna-seqc-python/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rna-seqc-python/meta.yaml b/recipes/rna-seqc-python/meta.yaml index c0cfabfddca36..5ed1a64d5e32e 100644 --- a/recipes/rna-seqc-python/meta.yaml +++ b/recipes/rna-seqc-python/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} source: - url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/rnaseqc-{{ version }}.tar.gz + url: https://pypi.org/packages/source/{{ pypi_name[0] }}/{{ pypi_name }}/rnaseqc-{{ version }}.tar.gz sha256: 857ad1ad54f2b563163d75ff8c5f2439208d06980b7c8ded279bd59d19c48a0f build: