Merge pull request #16 from cokelaer/fix_CI

Fixing CI
sequana · Jun 29, 2022 · c8d0873 · c8d0873
2 parents 56fc104 + ec2caf1
commit c8d0873
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Showing 3 changed files with 21 additions and 3 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -6,6 +6,8 @@ on:
       - master
   pull_request:
     branches-ignore: []
+  schedule:
+    - cron: '0 0 * * SUN'
 
 jobs:
   build-linux:
@@ -35,12 +37,12 @@ jobs:
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
-        conda update ruamel_yaml
+        #conda update ruamel_yaml
 
     - name: conda
       run: |
-        conda install -c conda-forge mamba --quiet
-        mamba install -c bioconda -c conda-forge -c bioconda --quiet -y bowtie samtools bamtools bedtools bowtie2 fastqc subread fastp deeptools
+        conda install -c conda-forge --quiet 'mamba<0.24' python=${{ matrix.python }}
+        mamba install -c bioconda -c conda-forge --quiet  --file environment.yml 
 
     - name: Install dependencies
       run: |

diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,14 @@
+cutadapt
+picard
+bowtie
+bowtie2
+STAR
+subread
+bamtools
+samtools
+deeptools
+gffread
+salmon
+fastp
+fastqc
+bedtools
diff --git a/sequana_pipelines/rnaseq/requirements.txt b/sequana_pipelines/rnaseq/requirements.txt
@@ -11,3 +11,5 @@
 - Rscript
 - fastp
 - fastqc
+- samtools
+- bamtools