From 2aa2f62af06213d3060378b5600c10d5e79787fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Felix=20M=C3=B6lder?= Date: Mon, 18 Sep 2023 10:38:27 +0200 Subject: [PATCH] fix: fix freebayes parallel (#1807) ### Description Freebayes parallel is once again failing due to issues with some of its dependencies. As a workaround htslib need to be pinned to v.1.16 as already described [here](https://github.com/bioconda/bioconda-recipes/issues/42643#issuecomment-1692969153). ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --- bio/freebayes/environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/bio/freebayes/environment.yaml b/bio/freebayes/environment.yaml index 6b906c6a3d..929f33008f 100644 --- a/bio/freebayes/environment.yaml +++ b/bio/freebayes/environment.yaml @@ -6,6 +6,7 @@ dependencies: - freebayes =1.3.6 - bcftools =1.15 # pinned to prevent conflicts with vcflib 1.0.3 - vcflib =1.0.3 # pinned because of bug in v1.0.9 (https://github.com/vcflib/vcflib/issues/389) + - htslib =1.16 # pinned because of bug (https://github.com/bioconda/bioconda-recipes/issues/42643#issuecomment-1692969153) - parallel =20230722 - bedtools =2.31.0 - sed =4.8