Merge pull request #830 from maxplanck-ie/dev_wd

Dev wd
maxplanck-ie · Aug 15, 2022 · 678ae47 · 678ae47
2 parents 912ad81 + 870d381
commit 678ae47
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diff --git a/.azure-pipelines/setup.yml b/.azure-pipelines/setup.yml
diff --git a/.azure-pipelines/testCreateEnv.py b/.azure-pipelines/testCreateEnv.py
diff --git a/.github/snakePipesEnvCI.yml b/.github/snakePipesEnvCI.yml
@@ -0,0 +1,15 @@
+name: snakePipes_CI
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.9
+  - snakemake=6.2.1
+  - fuzzywuzzy
+  - mock
+  - sphinx=4.2.0
+  - sphinx-argparse
+  - sphinx_rtd_theme=1.0.0
+  - flake8
+  - coreutils
+  - mamba
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -0,0 +1,100 @@
+name: linux
+
+on: 
+  pull_request:
+
+defaults:
+  run:
+      shell: bash -l {0}
+
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: .github/snakePipesEnvCI.yml
+        cache-downloads: true
+    - name: Install snakePipes
+      run: |
+        micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
+    - name: docs
+      run: |
+        micromamba activate snakePipes_CI
+        cd docs
+        make html
+  flake:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: .github/snakePipesEnvCI.yml
+        cache-downloads: true
+    - name: Install snakePipes
+      run: |
+        micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
+    - name: flake
+      run: |
+        micromamba activate snakePipes_CI
+        flake8 --ignore=E501,E722,E402 --exclude docs/conf.py .
+  CI:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: .github/snakePipesEnvCI.yml
+        cache-downloads: true
+        channel-priority: 'flexible'
+    - name: Install snakePipes
+      run: |
+        micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
+    - name: CI
+      run: |
+        micromamba activate snakePipes_CI
+        ./.ci_stuff/test_dag.sh
+  createEnvs:
+    needs: CI
+    strategy:
+      fail-fast: false
+      matrix:
+        envs: [
+          'CONDA_SHARED_ENV',
+          'CONDA_CREATE_INDEX_ENV',
+          'CONDA_RNASEQ_ENV',
+          'CONDA_RMATS_ENV',
+          'CONDA_scRNASEQ_ENV',
+          'CONDA_seurat3_ENV',
+          'CONDA_loompy_ENV',
+          'CONDA_alevinqc_ENV',
+          'CONDA_eisaR_ENV',
+          'CONDA_DNA_MAPPING_ENV',
+          'CONDA_CHIPSEQ_ENV',
+          'CONDA_ATAC_ENV',
+          'CONDA_HIC_ENV',
+          'CONDA_WGBS_ENV',
+          'CONDA_RMD_ENV',
+          'CONDA_PREPROCESSING_ENV',
+          'CONDA_NONCODING_RNASEQ_ENV',
+          'CONDA_SAMBAMBA_ENV',
+          'CONDA_pysam_ENV'
+        ]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: .github/snakePipesEnvCI.yml
+        cache-downloads: true
+    - name: install snakePipes
+      run: |
+        micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
+    - name: createEnvs
+      run: |
+        micromamba activate snakePipes_CI
+        conda config --set channel_priority flexible
+        snakePipes createEnvs --force --only ${{matrix.envs}}
+
diff --git a/.github/workflows/osx.yml b/.github/workflows/osx.yml
@@ -0,0 +1,51 @@
+name: osx
+
+on:
+  pull_request:
+
+defaults:
+  run:
+      shell: bash -l {0}
+
+jobs:
+  createEnvs_OSX:
+    strategy:
+      fail-fast: false
+      matrix:
+        envs: [
+          'CONDA_SHARED_ENV',
+          'CONDA_CREATE_INDEX_ENV',
+          'CONDA_RNASEQ_ENV',
+          'CONDA_RMATS_ENV',
+          'CONDA_scRNASEQ_ENV',
+          'CONDA_seurat3_ENV',
+          'CONDA_loompy_ENV',
+          'CONDA_alevinqc_ENV',
+          'CONDA_eisaR_ENV',
+          'CONDA_DNA_MAPPING_ENV',
+          'CONDA_CHIPSEQ_ENV',
+          'CONDA_ATAC_ENV',
+          'CONDA_HIC_ENV',
+          'CONDA_WGBS_ENV',
+          'CONDA_RMD_ENV',
+          'CONDA_PREPROCESSING_ENV',
+          'CONDA_NONCODING_RNASEQ_ENV',
+          'CONDA_SAMBAMBA_ENV',
+          'CONDA_pysam_ENV'
+        ]
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: .github/snakePipesEnvCI.yml
+          cache-downloads: true
+      - name: install snakePipes_OSX
+        run: |
+          micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
+      - name: createEnvsOSX
+        run: |
+          micromamba activate snakePipes_CI
+          conda config --set channel_priority flexible
+          snakePipes createEnvs --force --only ${{matrix.envs}}
+     
diff --git a/.gitignore b/.gitignore
@@ -24,4 +24,5 @@ _sources
 /snakePipes/shared/rscripts/*.html
 output
 
+# pip stuff
 snakePipes.egg-info
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
diff --git a/snakePipes/shared/rules/envs/wgbs.yaml b/snakePipes/shared/rules/envs/wgbs.yaml
@@ -12,7 +12,7 @@ dependencies:
   - r-base = 3.6.3
   - r-car = 3.0_6
   - r-factominer = 2.2
-  - r-ggplot2 = 3.1.1
+  - r-ggplot2
   - r-rmarkdown
   - r-dplyr = 1.0.2
   - r-tidyr