Need to tweak trimmomatic.py

Dockerfile

@@ -399,10 +399,8 @@ RUN curl -L -s -o shi7.tar.gz https://github.com/knights-lab/shi7/archive/refs/t
    pip3 install --no-cache-dir shi7.tar.gz && \
    rm shi7.tar.gz
    
-# Fiddle with trimmomatic so shi7 is happy
-RUN curl -L -s -o /opt/bin/trimmomatic https://raw.githubusercontent.com/bioconda/bioconda-recipes/master/recipes/trimmomatic/trimmomatic.py && \
-   chmod 555 /opt/bin/trimmomatic && \
-   ln -s /usr/share/java/trimmomatic-0.39.jar /opt/bin/trimmomatic.jar
+# Use trimmomatic.py from bioconda to make shi7 happy
+COPY trimmomatic.py /opt/bin/trimmomatic
 
 # --------------------
 # Final apt cleanup

trimmomatic.py

-#!/usr/bin/env python
+#!/usr/bin/env python3
 #
 # Wrapper script for Java Conda packages that ensures that the java runtime
 # is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128).
 
+# This script modified from https://raw.githubusercontent.com/bioconda/bioconda-recipes/master/recipes/trimmomatic/trimmomatic.py
+
 #
 # Program Parameters
 #
@@ -85,7 +87,7 @@ def main():
     we copy the jar file, lib, and resources to the exec_dir directory.
     """
     (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:])
-    jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0])
+    jar_dir = exec_dir if exec_dir else "/usr/share/java/"
 
     if pass_args != [] and pass_args[0].startswith('eu'):
         jar_arg = '-cp'