From 8e3fc49a3540f805f65fe2ceba8c4fa2197093fc Mon Sep 17 00:00:00 2001 From: VinzentRisch Date: Thu, 5 Dec 2024 15:15:48 +0100 Subject: [PATCH 1/3] modify env file --- ...amrfinderplus-qiime2-pathogenome-2024.10.yml | 10 ++++++++++ .../q2-amrfinderplus-qiime2-tiny-2024.10.yml | 17 ----------------- 2 files changed, 10 insertions(+), 17 deletions(-) create mode 100644 environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml delete mode 100644 environments/q2-amrfinderplus-qiime2-tiny-2024.10.yml diff --git a/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml b/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml new file mode 100644 index 0000000..9ac9a4e --- /dev/null +++ b/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml @@ -0,0 +1,10 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released +- conda-forge +- bioconda +dependencies: + - qiime2-pathogenome + - ncbi-amrfinderplus + - pip + - pip: + - "q2-amrfinderplus @ git+https://github.com/bokulich-lab/q2-amrfinderplus.git" diff --git a/environments/q2-amrfinderplus-qiime2-tiny-2024.10.yml b/environments/q2-amrfinderplus-qiime2-tiny-2024.10.yml deleted file mode 100644 index 6c1ba3d..0000000 --- a/environments/q2-amrfinderplus-qiime2-tiny-2024.10.yml +++ /dev/null @@ -1,17 +0,0 @@ -name: q2-amrfinderplus-qiime2-tiny-2024.10 -channels: -- https://packages.qiime2.org/qiime2/2024.10/tiny/passed -- conda-forge -- bioconda -dependencies: - - qiime2-tiny - # Note 1: Add any additional conda dependencies here. - - pip - - pip: - # Note 2: Add any additional pip dependencies here. - # - # some pip dependency - # Note 3: If you host your repository on GitHub, and you uncomment and modify - # the following lines to replace REPO-OWNER with the user or organization - # name that owns the repository, your installation commands can be updated to - # install from this file without additional steps. - # - "q2-amrfinderplus @ git+https://github.com/REPO-OWNER/q2-amrfinderplus.git" From 4dbe8e71867a83ae5741d6d5e71b28826ff015a6 Mon Sep 17 00:00:00 2001 From: VinzentRisch Date: Thu, 5 Dec 2024 15:32:02 +0100 Subject: [PATCH 2/3] changed ci --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5c79320..dc819bd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,7 +7,7 @@ on: branches: ["main"] jobs: - build-and-test-qiime2-tiny-2024-10: + build-and-test-qiime2-pathogenome-2024-10: runs-on: ${{ matrix.os }} strategy: matrix: @@ -19,8 +19,8 @@ jobs: - name: Set up Conda uses: conda-incubator/setup-miniconda@v3 with: - activate-environment: q2-amrfinderplus-qiime2-tiny-2024.10 - environment-file: environments/q2-amrfinderplus-qiime2-tiny-2024.10.yml + activate-environment: q2-amrfinderplus-qiime2-pathogenome-2024.10 + environment-file: environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml auto-activate-base: false - name: Install plugin From be18cb097c576d444010a9e995a1b09255305ea4 Mon Sep 17 00:00:00 2001 From: VinzentRisch Date: Thu, 5 Dec 2024 15:52:00 +0100 Subject: [PATCH 3/3] removed the dependecy in env file --- environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml b/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml index 9ac9a4e..c41a02e 100644 --- a/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml +++ b/environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml @@ -4,7 +4,6 @@ channels: - bioconda dependencies: - qiime2-pathogenome - - ncbi-amrfinderplus - pip - pip: - "q2-amrfinderplus @ git+https://github.com/bokulich-lab/q2-amrfinderplus.git"