From 6e49c1b00e6e89eb782e7d43d0bd3b601b22e926 Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Tue, 10 Dec 2024 11:31:37 +0800
Subject: [PATCH] try manually installing syri dependencies from pypi

---
 .github/workflows/build.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index c3d8dae..b556b4b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -30,7 +30,9 @@ jobs:
         python -m pip install --upgrade pip setuptools
         # apparently the runners all have conda installed
         # use that to install syri, as it isn't on pypi
-        $CONDA/bin/conda install -c conda-forge -c bioconda "syri>=1.6.5"
+        # manually install syris dependencies, conda does not install
+        pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
+        $CONDA/bin/conda install --freeze-installed --no-deps -c conda-forge -c bioconda "syri>=1.6.5"
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Build package
       run: pip install .