added pydeseq2 dependency

saezlab · May 7, 2024 · 0f3f381 · 0f3f381
1 parent 813e925
commit 0f3f381
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -6,6 +6,9 @@ on:
 
 jobs:
   build-linux:
+    defaults:
+      run:
+        shell: bash -l {0}
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4

diff --git a/environment.yml b/environment.yml
@@ -1,16 +1,13 @@
 name: networkcommons_test
 channels:
   - bioconda
-  - r
   - conda-forge
   - defaults
 dependencies:
-  - bioconductor-deseq2=1.42.0
   - graphviz=2.50.0
   - pip=24.0
   - python=3.10.14
   - python-graphviz=0.20.3
-  - r-base=4.3.1
   - setuptools=69.5.1
   - pip:
       - cvxpy==1.4.3
@@ -21,6 +18,7 @@ dependencies:
       - omnipath==1.0.8
       - pathos==0.3.2
       - picos==2.4.17
+      - pydeseq2==0.4.9
       - pyocclient==0.6
       - pytest==8.2.0
       - pytest-cov==5.0.0