many changes ;-)

Former-commit-id: cb4aea844e960e4af4dc673ebc8eec49a7d12b13

obitools4/Dockerfile

@@ -0,0 +1,31 @@
+FROM ubuntu:lunar as builder
+LABEL dockerfile.version="1"
+LABEL software="obitools4"
+
+WORKDIR /
+RUN apt update  --fix-missing && apt upgrade -y
+RUN apt install -y build-essential 
+RUN apt install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
+# RUN git clone https://git.metabarcoding.org/org-asm/org-annotate.git
+# RUN cd org-annotate/src && make && cd ../..
+# RUN cd /org-annotate/data/its/ITSx_db/HMMs && \
+#     rm *.h3* && \
+#     for f in *.hmm ; do /org-annotate/ports/i386-linux/bin/hmmpress $f ; done
+
+RUN apt install -y python3-pip python3-dev python3-venv
+RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
+RUN cd org-asm 
+RUN python3 -m venv ../org-assembler 
+RUN bash -c '../org-assembler/bin/pip3 install -r /org-asm/requirements.txt'
+RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity'
+RUN cd ..
+
+
+# FROM ubuntu:lunar as phyloskims
+# WORKDIR /
+# RUN apt update  --fix-missing && apt upgrade -y
+# RUN apt install -y tcsh bash gawk parallel zlib1g libglib2.0-0
+# COPY --from=builder /org-annotate /org-annotate
+# RUN rm -rf /org-annotate/src
+# COPY --from=builder /org-assembler /org-assembler
+# RUN mkdir -p /data