From 3940444346c2b600124160b1d10d3d5798cb1382 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Arnoux?= <39793176+jpjarnoux@users.noreply.github.com> Date: Tue, 23 Jan 2024 09:48:44 +0100 Subject: [PATCH 1/4] Update check_recipes.yml .condarc.yml has been removed so I update the check --- .github/workflows/check_recipes.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/check_recipes.yml b/.github/workflows/check_recipes.yml index 49f3fb89..e5965957 100644 --- a/.github/workflows/check_recipes.yml +++ b/.github/workflows/check_recipes.yml @@ -26,13 +26,12 @@ jobs: # Setting up miniconda - uses: conda-incubator/setup-miniconda@v2 with: - condarc-file: .condarc.yml activate-environment: test python-version: ${{ matrix.python-version }} - name: Set up test environment shell: bash -l {0} run: | - conda install -y ppanggolin + conda install -c conda-forge -c bioconda -y ppanggolin - name: check installation shell: bash -l {0} run: | From f16888e347d0ff68a161849ecd3eed18d9e8f0ed Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 23 Jan 2024 10:25:08 +0100 Subject: [PATCH 2/4] add channels to miniconda action --- .github/workflows/check_recipes.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_recipes.yml b/.github/workflows/check_recipes.yml index e5965957..10eb25e8 100644 --- a/.github/workflows/check_recipes.yml +++ b/.github/workflows/check_recipes.yml @@ -26,8 +26,8 @@ jobs: # Setting up miniconda - uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: test python-version: ${{ matrix.python-version }} + channels: conda-forge,bioconda,defaults - name: Set up test environment shell: bash -l {0} run: | From b6152baac6ee74dc9173391fe2459861cb95a5ed Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 23 Jan 2024 10:44:25 +0100 Subject: [PATCH 3/4] add defaults channel in install docs --- README.md | 2 +- docs/user/install.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 04ba2af5..958d2c28 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ To ensure a smoother installation and avoid conflicting dependencies, it's highl ```bash # Install PPanGGOLiN into a new conda environment -conda create -n ppanggolin -c conda-forge -c bioconda ppanggolin +conda create -n ppanggolin -c defaults -c conda-forge -c bioconda ppanggolin # Check PPanGGOLiN install conda activate ppanggolin diff --git a/docs/user/install.md b/docs/user/install.md index 260b496d..40172657 100644 --- a/docs/user/install.md +++ b/docs/user/install.md @@ -11,7 +11,7 @@ To ensure a smoother installation and avoid conflicting dependencies, it's highl ```bash # Install into a new conda environment -conda create -n ppanggo -c conda-forge -c bioconda ppanggolin +conda create -n ppanggo -c defaults -c conda-forge -c bioconda ppanggolin # Check PPanGGOLiN install conda activate ppanggo From 6da4c3c974bce7693c3e396c0342a154839928b4 Mon Sep 17 00:00:00 2001 From: Jean Mainguy Date: Wed, 24 Jan 2024 12:18:59 +0100 Subject: [PATCH 4/4] rm channel in install command as they are already set in action setup --- .github/workflows/check_recipes.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_recipes.yml b/.github/workflows/check_recipes.yml index 10eb25e8..53fdbf93 100644 --- a/.github/workflows/check_recipes.yml +++ b/.github/workflows/check_recipes.yml @@ -31,7 +31,7 @@ jobs: - name: Set up test environment shell: bash -l {0} run: | - conda install -c conda-forge -c bioconda -y ppanggolin + conda install -y ppanggolin - name: check installation shell: bash -l {0} run: |