diff --git a/bioconda_utils/bioconda_utils-requirements.txt b/bioconda_utils/bioconda_utils-requirements.txt index ec26046ffb..93d9f41bb5 100644 --- a/bioconda_utils/bioconda_utils-requirements.txt +++ b/bioconda_utils/bioconda_utils-requirements.txt @@ -27,6 +27,7 @@ conda-forge-pinning=2022.08.25.15.20.42 # tools anaconda-client=1.6.* # anaconda_upload +galaxy-tool-util # mulled test and container build involucro=1.1.* # mulled test and container build skopeo=0.1.35 # docker upload git=2.* # well - git @@ -52,7 +53,6 @@ pyjwt>=2.4.0 # githubhandler (JWT signing), needs >=2.4.0, CVE-2022 # unknown beautifulsoup4=4.6.* -galaxy-lib>=18.9.1 jinja2>=2.10.1,<3 markupsafe<2.1 # markupsafe 2.1 breaks jinja2 diff --git a/bioconda_utils/pkg_test.py b/bioconda_utils/pkg_test.py index 374a02c0f2..469ecbc4b2 100644 --- a/bioconda_utils/pkg_test.py +++ b/bioconda_utils/pkg_test.py @@ -156,12 +156,13 @@ def test_package( cmd += channel_args cmd += shlex.split(mulled_args) - # galaxy-lib always downloads involucro, unless it's in cwd or its path is explicitly given. # We inject a POSTINSTALL to the involucro command with a small wrapper to # create activation / entrypoint scripts for the container. involucro_path = os.path.join(os.path.dirname(__file__), 'involucro') if not os.path.exists(involucro_path): raise RuntimeError('internal involucro wrapper missing') + # Explicitly pass --involucro-path since otherwise mulled always downloads + # involucro (unless it is in the cwd). cmd += ['--involucro-path', involucro_path] logger.debug('mulled-build command: %s' % cmd) diff --git a/docs/source/contributor/build-system.rst b/docs/source/contributor/build-system.rst index 9caa4a0313..8a9b2fe586 100644 --- a/docs/source/contributor/build-system.rst +++ b/docs/source/contributor/build-system.rst @@ -95,7 +95,7 @@ N.B., due to transitioning to Azure, the remainder of this section is no longer - Upon successfully building and testing via ``conda-build``, the built package is added to a minimal BusyBox container using ``mulled-build`` (maintained in - `galaxy-lib `_). This acts as + `galaxy `_). This acts as a more stringent test than ``conda-build`` alone. The BusyBox container purposefully is missing many system libraries (like libgcc) that may be present in the CentOS 7 container. Note that it is common for a package to