Add autoreconf build script

.github/workflows/autoreconf.yml

@@ -0,0 +1,29 @@
+name: Autoreconf Mirror Branch
+
+on:
+  push:
+    branches: [ main ]
+
+jobs:
+  autoreconf:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Main Branch
+      uses: actions/checkout@v2
+      with:
+        ref: 'main'
+
+    - name: Set up Autotools
+      run: sudo apt-get update && sudo apt-get install -y autoconf automake libtool
+
+    - name: Run autoreconf
+      run: autoreconf -i
+
+    - name: Push to Mirror Branch
+      run: |
+        git config --global user.name 'GitHub Action'
+        git config --global user.email 'action@github.com'
+        git add -A
+        git commit -m "Auto-update Autotools files" || echo "No changes to commit"
+        git push origin HEAD:main-build -f

conda/benj.yml.in

@@ -81,6 +81,8 @@ dependencies:
   - conda-forge::openai
   - bioconda::snakemake
   - bioconda::nextflow
+  - bioconda::plink
+  - bioconda::plink2
   ## plots
   - conda-forge::seaborn
   - conda-forge::matplotlib<3.7
@@ -122,6 +124,7 @@ dependencies:
   - bioconda::bioconductor-genomeinfodb
   - bioconda::bioconductor-bsgenome
   - bioconda::bioconductor-bsgenome.hsapiens.ucsc.hg38
+  - bioconda::bioconductor-snplocs.hsapiens.dbsnp151.grch38
   - bioconda::bioconductor-bsgenome.mmusculus.ucsc.mm10
   - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
   - bioconda::bioconductor-txdb.mmusculus.ucsc.mm10.knowngene