diff --git a/.gitignore b/.gitignore index bccd48d..120aeb0 100644 --- a/.gitignore +++ b/.gitignore @@ -130,4 +130,6 @@ dmypy.json .pyre/ # IDE -.vscode/ \ No newline at end of file +.vscode/ + +test* \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 8976a88..2ad204a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [0.6.8](https://github.com/RIVM-bioinformatics/SARS2seq/compare/v0.6.7...v0.6.8) (2024-07-03) + + +### Dependencies + +* Update conda environment files to remove the 'intel' channel ([4572252](https://github.com/RIVM-bioinformatics/SARS2seq/commit/4572252e6114937ce05ffd2e8fae60602cc0582a)) + + +### Documentation + +* update documentation page accordingly ([4572252](https://github.com/RIVM-bioinformatics/SARS2seq/commit/4572252e6114937ce05ffd2e8fae60602cc0582a)) + ## [0.6.7](https://github.com/RIVM-bioinformatics/SARS2seq/compare/v0.6.6...v0.6.7) (2024-04-04) diff --git a/SARS2seq/version.py b/SARS2seq/version.py index f6104e0..afd45a4 100644 --- a/SARS2seq/version.py +++ b/SARS2seq/version.py @@ -1 +1 @@ -__version__ = "0.6.7" +__version__ = "0.6.8" diff --git a/SARS2seq/workflow/envs/Alignment.yaml b/SARS2seq/workflow/envs/Alignment.yaml index 42d1cda..fbeedbe 100644 --- a/SARS2seq/workflow/envs/Alignment.yaml +++ b/SARS2seq/workflow/envs/Alignment.yaml @@ -2,7 +2,6 @@ name: Reference_alignment channels: - bioconda - conda-forge - - intel - nodefaults dependencies: - python=3.7 diff --git a/SARS2seq/workflow/envs/Clean.yaml b/SARS2seq/workflow/envs/Clean.yaml index 2a4ef0b..be139c3 100644 --- a/SARS2seq/workflow/envs/Clean.yaml +++ b/SARS2seq/workflow/envs/Clean.yaml @@ -2,7 +2,6 @@ name: QC_and_cleanup channels: - bioconda - conda-forge - - intel - nodefaults dependencies: - python=3.8 diff --git a/SARS2seq/workflow/envs/Consensus.yaml b/SARS2seq/workflow/envs/Consensus.yaml index 4e18609..c5b6db2 100644 --- a/SARS2seq/workflow/envs/Consensus.yaml +++ b/SARS2seq/workflow/envs/Consensus.yaml @@ -2,7 +2,6 @@ name: Consensus channels: - bioconda - conda-forge - - intel - nodefaults dependencies: - python=3.7 diff --git a/SARS2seq/workflow/envs/Mutations.yaml b/SARS2seq/workflow/envs/Mutations.yaml index c1917de..00f3171 100644 --- a/SARS2seq/workflow/envs/Mutations.yaml +++ b/SARS2seq/workflow/envs/Mutations.yaml @@ -2,7 +2,6 @@ name: Mutations channels: - bioconda - conda-forge - - intel - nodefaults dependencies: - bcftools==1.14 \ No newline at end of file diff --git a/SARS2seq/workflow/envs/Typing.yaml b/SARS2seq/workflow/envs/Typing.yaml index 2c84a69..85785eb 100644 --- a/SARS2seq/workflow/envs/Typing.yaml +++ b/SARS2seq/workflow/envs/Typing.yaml @@ -2,7 +2,6 @@ name: Typing channels: - bioconda - conda-forge - - intel - nodefaults dependencies: - python=3.7 diff --git a/docs/index.md b/docs/index.md index 5199f9a..2abac62 100644 --- a/docs/index.md +++ b/docs/index.md @@ -36,10 +36,7 @@ git clone https://github.com/RIVM-bioinformatics/SARS2seq.git; cd SARS2seq; git 1. Create the required conda-environment and install the necessary dependencies. Copy and paste the code-snippet below in order to create the new conda-environment and directly activate it. - `conda create --name SARS2seq -c conda-forge mamba python=3.7 -y; conda activate SARS2seq; mamba env update -f mamba-env.yaml` - - You can also use the following snippet if the code-snippet above didn't work for you: - `conda env create -f env.yml && conda activate SARS2seq` + `mamba env create -f env.yml && conda activate SARS2seq` **The "SARS2seq" environment should now be active** diff --git a/env.yml b/env.yml index b770c5c..78c0ad6 100644 --- a/env.yml +++ b/env.yml @@ -2,7 +2,6 @@ name: SARS2seq channels: - bioconda - conda-forge - - intel - nodefaults dependencies: - python=3.8 diff --git a/mamba-env.yaml b/mamba-env.yaml deleted file mode 100644 index eaedca1..0000000 --- a/mamba-env.yaml +++ /dev/null @@ -1,16 +0,0 @@ -channels: - - bioconda - - conda-forge - - intel -dependencies: - - python=3.7 - - conda=4.11 - - mamba - - drmaa==0.7.9 - - snakemake==7.12.1 - - tabulate==0.8.10 - - biopython==1.79 - - pyyaml==6.0 - - urllib3>=1.26 - - fpdf==1.7.2 - - pip