Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

chore: sync main to dev #73

Open
wants to merge 3 commits into
base: dev
Choose a base branch
from
Open

chore: sync main to dev #73

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
4572252
deps: Update conda environment files to remove the 'intel' channel
florianzwagemaker Jul 3, 2024
b757c55
chore(main): release 0.6.8
ids-bioinformatics Jul 3, 2024
113a6de
Merge pull request #72 from RIVM-bioinformatics/release-please--branc…
florianzwagemaker Jul 3, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -130,4 +130,6 @@ dmypy.json
.pyre/

# IDE
.vscode/
.vscode/

test*
12 changes: 12 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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)


Expand Down
2 changes: 1 addition & 1 deletion SARS2seq/version.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.6.7"
__version__ = "0.6.8"
1 change: 0 additions & 1 deletion SARS2seq/workflow/envs/Alignment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: Reference_alignment
channels:
- bioconda
- conda-forge
- intel
- nodefaults
dependencies:
- python=3.7
Expand Down
1 change: 0 additions & 1 deletion SARS2seq/workflow/envs/Clean.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: QC_and_cleanup
channels:
- bioconda
- conda-forge
- intel
- nodefaults
dependencies:
- python=3.8
Expand Down
1 change: 0 additions & 1 deletion SARS2seq/workflow/envs/Consensus.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: Consensus
channels:
- bioconda
- conda-forge
- intel
- nodefaults
dependencies:
- python=3.7
Expand Down
1 change: 0 additions & 1 deletion SARS2seq/workflow/envs/Mutations.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: Mutations
channels:
- bioconda
- conda-forge
- intel
- nodefaults
dependencies:
- bcftools==1.14
1 change: 0 additions & 1 deletion SARS2seq/workflow/envs/Typing.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: Typing
channels:
- bioconda
- conda-forge
- intel
- nodefaults
dependencies:
- python=3.7
Expand Down
5 changes: 1 addition & 4 deletions docs/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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**

Expand Down
1 change: 0 additions & 1 deletion env.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: SARS2seq
channels:
- bioconda
- conda-forge
- intel
- nodefaults
dependencies:
- python=3.8
Expand Down
16 changes: 0 additions & 16 deletions mamba-env.yaml
View file
Open in desktop

This file was deleted.

Loading