diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 71b0147428ff8..6269705631657 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -60,7 +60,7 @@ jobs: fail-fast: false max-parallel: 4 matrix: - runner: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9] + runner: [0, 1, 2, 3, 4, 5, 6, 7] steps: - uses: actions/checkout@v1 @@ -117,6 +117,6 @@ jobs: python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 10 \ + --worker-offset ${{ matrix.runner }} --n-workers 8 \ --anaconda-upload conda clean -y --all diff --git a/recipes/ncbi-vdb/build.sh b/recipes/ncbi-vdb/build.sh index e9bd1c2f7fa1b..0c80dbdffb142 100644 --- a/recipes/ncbi-vdb/build.sh +++ b/recipes/ncbi-vdb/build.sh @@ -1,3 +1,5 @@ +#!/bin/bash +set -e # For inspiration, see also Debian's ncbi-vdb package: # https://salsa.debian.org/med-team/ncbi-vdb @@ -12,11 +14,11 @@ sed -i.backup \ # * --debug lets the configure script print extra info # * Only LDFLAGS and CXX can be customized at configure time. +./configure --help ./configure \ --debug \ --prefix=$PREFIX \ --build-prefix=ncbi-outdir \ - --with-ngs-sdk-prefix=$PREFIX \ CXX=$CXX # Edit the generated build configuration to use the proper tools @@ -27,7 +29,7 @@ sed -i.backup \ # -e "s|= ar|= $AR|" \ # build/Makefile.config.linux.x86_64 -make +make CC=$CC # This does not install the header files make install @@ -36,7 +38,10 @@ make install make -C test/vdb # Copy headers manually. As done by Debian, install them into a common subdirectory -mv interfaces/* $PREFIX/include/ncbi-vdb +ls interfaces +for f in interfaces/* ; do + mv $f $PREFIX/include/ncbi-vdb +done # To Do diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 804564bd10d9d..5ef20ef023c5a 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "2.11.0" %} -{% set sha256 = "9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa" %} +{% set version = "3.0.0" %} +{% set sha256 = "154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7" %} package: name: ncbi-vdb version: {{ version }} build: - number: 1 + number: 0 source: url: https://github.com/ncbi/ncbi-vdb/archive/{{ version }}.tar.gz @@ -20,6 +20,7 @@ source: requirements: build: - make + - cmake - {{ compiler('c') }} - {{ compiler('cxx') }} host: