Merge pull request #885 from maxplanck-ie/fix884

Fix #884
maxplanck-ie · Mar 28, 2023 · 4b2d1a7 · 4b2d1a7
2 parents a591948 + 0d8e030
commit 4b2d1a7
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Showing 9 changed files with 30 additions and 9 deletions.
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -75,6 +75,7 @@ jobs:
           'CONDA_ATAC_ENV',
           'CONDA_HIC_ENV',
           'CONDA_WGBS_ENV',
+          'CONDA_DSS_ENV',
           'CONDA_RMD_ENV',
           'CONDA_PREPROCESSING_ENV',
           'CONDA_NONCODING_RNASEQ_ENV',
@@ -94,6 +95,6 @@ jobs:
     - name: createEnvs
       run: |
         micromamba activate snakePipes_CI
-        conda config --set channel_priority flexible
+        conda config --set channel_priority strict
         snakePipes createEnvs --force --only ${{matrix.envs}}
 
diff --git a/.github/workflows/osx.yml b/.github/workflows/osx.yml
@@ -26,6 +26,7 @@ jobs:
           'CONDA_ATAC_ENV',
           'CONDA_HIC_ENV',
           'CONDA_WGBS_ENV',
+          'CONDA_DSS_ENV',
           'CONDA_RMD_ENV',
           'CONDA_PREPROCESSING_ENV',
           'CONDA_NONCODING_RNASEQ_ENV',
@@ -45,6 +46,6 @@ jobs:
       - name: createEnvsOSX
         run: |
           micromamba activate snakePipes_CI
-          conda config --set channel_priority flexible
+          conda config --set channel_priority strict
           snakePipes createEnvs --force --only ${{matrix.envs}}
      
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.7.2
+  version: 2.7.3
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,6 +1,12 @@
 snakePipes News
 ===============
 
+snakePipes 2.7.3
+----------------
+
+* Fixes #884 by creating an additional conda env for DSS. Build tests are now run with strict channel priority.
+
+
 snakePipes 2.7.2
 ----------------
 * STAR version has been updated to 2.7.10b. 2.7.10a was returning segmentation fault on MAC.

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.7.2'
+__version__ = '2.7.3'
diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py
@@ -34,6 +34,7 @@ def set_env_yamls():
             'CONDA_ATAC_ENV': 'envs/atac_seq.yaml',
             'CONDA_HIC_ENV': 'envs/hic.yaml',
             'CONDA_WGBS_ENV': 'envs/wgbs.yaml',
+            'CONDA_DSS_ENV': 'envs/wgbs_dss.yaml',
             'CONDA_RMD_ENV': 'envs/rmarkdown.yaml',
             'CONDA_PREPROCESSING_ENV': 'envs/preprocessing.yaml',
             'CONDA_NONCODING_RNASEQ_ENV': 'envs/noncoding.yaml',

diff --git a/snakePipes/shared/rules/WGBS.snakefile b/snakePipes/shared/rules/WGBS.snakefile
@@ -376,7 +376,7 @@ rule DSS:
         FDR=FDR
     threads: lambda wildcards: 10 if 10<max_thread else max_thread
     benchmark: '{}/.benchmark/DSS.benchmark'.format(get_outdir("DSS", None, minCoverage))
-    conda: CONDA_WGBS_ENV
+    conda: CONDA_DSS_ENV
     script: "../rscripts/WGBS_DSS.Rmd"
 
 

diff --git a/snakePipes/shared/rules/envs/wgbs.yaml b/snakePipes/shared/rules/envs/wgbs.yaml
@@ -18,12 +18,8 @@ dependencies:
   - r-dplyr
   - r-tidyr
   - r-pander
-  - r-factominer
-  - bioconductor-bsseq
   - bioconductor-genomicranges
   - bioconductor-genomicfeatures
-  - bioconductor-biomart
-  - bioconductor-dss
   - bioconductor-dmrseq
   - bioconductor-rtracklayer
   - bioconductor-biocparallel
diff --git a/snakePipes/shared/rules/envs/wgbs_dss.yaml b/snakePipes/shared/rules/envs/wgbs_dss.yaml
@@ -0,0 +1,16 @@
+name: WGBS_DSS-env-2.0
+channels:
+  - mpi-ie
+  - conda-forge
+  - bioconda
+dependencies:
+  - r-base
+  - r-car
+  - r-factominer
+  - r-ggplot2
+  - r-rmarkdown
+  - r-dplyr
+  - r-tidyr
+  - r-pander
+  - bioconductor-dss
+  - bioconductor-biocparallel