$ apptainer pull https://github.com/bast/apptainer-conda/releases/download/0.7.0/conda.sif Usage Reads the Conda environment fileenvironment.yml. Creates the folderenvironment. Runmyscript.pyinside the Conda environment defined byenvironment.yml: ...
The changes introduce two functions,has_apptainer()andhas_conda(), to check for the availability of Apptainer and Conda executables. New pytest markers,apptainerandconda, are defined to conditionally skip tests based on the presence of these tools. Various test functions intests/tests.pyare updat...
How to set apptainer shell when using --software-deployment-method apptainer with Snakemake? Currently, it is possible to set the shell for all rules using e.g. shell.executable("sh") somewhere before your first rule in the Snakefile. However, for your case, it would be better to ......
Apptainer/Singularity使用方法记录 在做生信分析的时候,难免会遇到一个pipeline上的软件存在冲突的情况,一般的解决方法是创建不同的conda环境,然后分别在不同的环境下跑不同的软件。这种操作可以解决环境冲突的问题但不适合写流程化的脚本,同时又非常占用空间。有的软件整合了pipeline流程的所有软件,按照顺序进行调用,这种...
使用apptainer构建容器时的R依赖性错误使用以下代码替换以“apt-get install -y --no-install-recommends...
def conda_prefix = ['singularity', 'apptainer'].contains(workflow.containerEngine) ? "export CONDA_PREFIX=/usr/local" : "" if (meta.single_end) { """ $conda_prefix ascp \\ $args \\ -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\ @@ -36,6 +39,8 @@ process ASPERA_CLI...
set_prompt.bash conda docker_ci examples framework large_media libmesh m4 modules petsc python scripts stork test tutorials unit .clang-format .coverage .editorconfig .gitattributes .gitignore .gitmodules .mailmap CODEOWNERS COPYING COPYRIGHT LICENSE README.md ...
{ MOOSE_TEST_TOOLS_VERSION }} CONDA_ALT_CHANNEL={{ CONDA_ALT_CHANNEL }} export MOOSE_JOBS={{ MOOSE_JOBS }} # Pinned versions MAMBAFORGE_VERSION=23.1.0-1 PYTHON_VERSION=3.10 # Install mamba in MOOSE_MAMBAFORGE curl -L https://github.com/conda-forge/miniforge/releases/download/${MAMBA...
I am trying to install Singularity 3.5.3 on an Ubuntu 18.04 VM instance. I have downloaded and installed go Version 1.13 and the Singularity source tarball on Github. When I try running ./mconfig, I get the error: markc@mark-vm:~/singula...
I'm trying to test out Singularity on our cluster - I am not an administrator of the cluster, and I don't have root. I created a few tar images on my laptop (Mac OSX, via vagrant), and sftp'ed them over to the cluster. On one of the clus...