From 4c067ae779d2a5c2c295dea313fbebc58ebdc011 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Mon, 18 Sep 2023 16:16:19 -0400
Subject: [PATCH] Adding cDNA_Cupcate to PYTHONPATH and suppressing sqanti
 depreciate warning

---
 docker/sqanti3/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docker/sqanti3/Dockerfile b/docker/sqanti3/Dockerfile
index 045e166..9ed796d 100644
--- a/docker/sqanti3/Dockerfile
+++ b/docker/sqanti3/Dockerfile
@@ -221,6 +221,7 @@ RUN mkdir -p /opt2/cdna_cupcake/28.0.0/ \
     && python setup.py install
 
 ENV PATH="${PATH}:/opt2/cdna_cupcake/28.0.0/cDNA_Cupcake-28.0.0/sequence"
+ENV PYTHONPATH="${PYTHONPATH}:/opt2/cdna_cupcake/28.0.0/cDNA_Cupcake-28.0.0/sequence"
 WORKDIR /opt2
 
 # Install R packages via apt 
@@ -293,4 +294,6 @@ WORKDIR /opt2
 ADD Dockerfile /opt2/sqanti3_5-1-2.dockerfile
 RUN chmod -R a+rX /opt2
 ENV PATH="/opt2:$PATH"
+# Hide deprecation warnings from sqanit
+ENV PYTHONWARNINGS="ignore::DeprecationWarning"
 WORKDIR /data2
\ No newline at end of file