Commit 70cf9fad authored by josh's avatar josh
Browse files

Need to tweak trimmomatic.py

parent 650a6942
Pipeline #211372 passed with stages
in 7 seconds
......@@ -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
......
#!/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'
......
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