Actualiser README.md

better check of format

.gitignore

@@ -0,0 +1,24 @@
+/OBITools-1.1.19/
+/OBITools-1.1.20/
+/OBITools-1.1.21/
+/OBITools-1.1.22/
+/OBITools-1.2.0/
+/obitools.test/
+/build/
+/dist/
+/OBITools-1.2.2/
+/OBITools-1.2.3/
+/OBITools-1.2.4/
+/OBITools-1.2.5/
+/OBITools-1.2.6/
+/OBITools-1.2.7/
+/OBITools-1.2.8/
+/OBITools-1.2.9/
+/OBITools-1.2.10/
+/.DS_Store
+/OBITools-1.2.11/
+/OBITools-1.2.12/
+/obitools.test.old/
+/coucou
+/toto.fasta
+/OBITools-1.2.13/

.pydevproject

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?eclipse-pydev version="1.0"?><pydev_project>
 <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
-<path>/obitools/src</path>
+<path>/OBITools-1.1/src</path>
 <path>/${PROJECT_DIR_NAME}/distutils.ext</path>
 </pydev_pathproperty>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>

Dockerfile

@@ -0,0 +1,102 @@
+FROM python:2.7.17-alpine AS builder
+
+RUN apk add --no-cache \
+    bash flex build-base curl openssl-dev bzip2-dev readline-dev sqlite-dev zlib-dev xz-dev tk-dev libffi-dev make ncurses-dev git
+
+RUN pip install Cython==0.29
+
+RUN mkdir -p /app
+WORKDIR /app
+COPY src .
+
+RUN gcc -o littlebigman littlebigman.c
+RUN python setup.py build_ext --inplace
+RUN python setup.py install
+RUN ./install.sh
+
+WORKDIR /app
+RUN git clone https://forge.metabarcoding.org/obitools/ecopcr.git
+WORKDIR /app/ecopcr/src
+RUN make clean && make \
+    && cp ecoPCR ecofind ecogrep /usr/local/bin
+
+WORKDIR /app
+RUN git clone https://forge.metabarcoding.org/obitools/ecoprimers.git
+WORKDIR /app/ecoprimers/src
+RUN make clean && make \
+    && cp ecoPrimers /usr/local/bin \
+    && cp ../tools/ecoPCRFormat.py /usr/local/bin/ecoPCRFormat \
+    && chmod +x /usr/local/bin/ecoPCRFormat
+
+WORKDIR /app
+RUN git clone --recurse-submodules https://forge.metabarcoding.org/obitools/sumatra.git
+WORKDIR /app/sumatra
+RUN make clean && make \
+    && cp sumatra /usr/local/bin 
+
+WORKDIR /app
+RUN git clone --recurse-submodules https://forge.metabarcoding.org/obitools/sumaclust.git
+WORKDIR /app/sumaclust
+RUN make clean && make \
+    && cp sumaclust /usr/local/bin 
+
+RUN find /usr/local/bin /usr/local/python2/bin /usr/local/python2/lib -type f -exec file {} \; | \
+    grep -E 'ELF (32-bit|64-bit) (executable|shared object)' | \
+    cut -d: -f1 | \
+    xargs -r strip --strip-unneeded || true
+
+RUN pip install "virtualenv<20" && \
+    virtualenv --system-site-packages /obitools-doc 
+    
+ENV PATH="/obitools-doc/bin:${PATH}"
+RUN pip install "sphinx==1.8.5"
+
+COPY doc /obitools-doc/doc
+
+RUN echo "/doc" > /obitools-doc/doc/sphinx/build_dir.txt
+
+ENV PYTHONPATH="/app"
+
+WORKDIR /obitools-doc/doc/sphinx
+RUN make html
+RUN cp /app/docserver.sh /usr/local/bin/docserver
+RUN chmod +x /usr/local/bin/docserver
+
+
+#--- Image finale minimaliste ---
+FROM python:2.7.17-alpine
+LABEL org.opencontainers.image.title="OBITools2 (legacy)"
+LABEL org.opencontainers.image.description="Legacy OBITools2 environment for compatibility with older pipelines and benchmarks. Includes OBITools2, ecoPCR, ecoPrimers, sumatra, and sumaclust. Python 2-based software stack. Full documentation embedded in the image."
+LABEL org.opencontainers.image.version="latest"
+LABEL org.opencontainers.image.authors="Eric Coissac <eric.coissac@metabarcoding.org>"
+LABEL org.opencontainers.image.url="https://registry.metabarcoding.org/image/obitools%2Fobitools2"
+LABEL org.opencontainers.image.documentation="https://metabarcoding.org/en/obitools/obitools2"
+LABEL org.opencontainers.image.source="https://forge.metabarcoding.org/obitools/obitools"
+
+# Dépendances runtime seulement (exemple)
+RUN apk add --no-cache \
+    openssl \
+    zlib \
+    libgomp
+
+# Copier Python compilé et libs depuis le builder
+COPY --from=builder /usr/local/lib/python2.7/site-packages /usr/local/lib/python2.7/site-packages
+COPY --from=builder /usr/local/bin /usr/local/bin
+COPY --from=builder /obitools-doc/doc/sphinx/build/html /doc
+
+RUN rm -rf /usr/local/share /usr/local/include /usr/local/lib/pkgconfig /usr/local/lib/python2.7/test && \
+    find /usr/local/bin /usr/local/python2/bin /usr/local/python2/lib -type f -exec file {} \; | \
+    grep -E 'ELF (32-bit|64-bit) (executable|shared object)' | \
+    cut -d: -f1 | \
+    xargs -r strip --strip-unneeded || true
+
+RUN mkdir -p /data 
+
+ENV LD_LIBRARY_PATH=/usr/local/lib
+ENV PATH="/usr/local/bin:${PATH}"
+
+VOLUME ["/data"]
+
+WORKDIR /data
+
+CMD ["ash"]

README.md

@@ -0,0 +1,11 @@
+# Legacy OBITools status
+
+Legacy OBITools is 20 years old. It was developed using Python 2, a language that is no longer supported. Therefore, maintaining this code is impossible. It has now been superseded by OBITools4, the latest version in the OBITools lineage.
+
+In order to enable users to continue using Legacy OBITools, a Docker image has been created and made available on the [metabarcoding.org registry](https://registry.metabarcoding.org). While we discourage using this old version for new projects, being able to run it can still be useful for reproducibility purposes.
+
+You can find more information about using this Docker image on the [relevant page](https://metabarcoding.org/en/obitools/obitools2) of the [new metabarcoding website](https://metabarcoding.org).
+
+All the best,
+
+Eric Coissac

distutils.ext/.gitignore

@@ -0,0 +1,2 @@
+*.pyc
+/.DS_Store

distutils.ext/obidistutils/.gitignore

@@ -0,0 +1 @@
+/*.pyc

distutils.ext/obidistutils/command/.gitignore

@@ -0,0 +1 @@
+/*.pyc

distutils.ext/obidistutils/command/build_sphinx.py

@@ -13,26 +13,29 @@ import sys
 
 try:
     from sphinx.setup_command import BuildDoc as ori_build_sphinx
+    
+    class build_sphinx(ori_build_sphinx):
+        '''
+        Build Sphinx documentation in html, epub and man formats 
+        '''
+
+        description = __doc__
+    
+        def run(self):
+            self.builder='html'
+            self.finalize_options()
+            ori_build_sphinx.run(self)
+            self.builder='epub'
+            self.finalize_options()
+            ori_build_sphinx.run(self)
+            self.builder='man'
+            self.finalize_options()
+            ori_build_sphinx.run(self)
+
 except ImportError:
     if not is_serenity() and install_requirements():
         log.info("Restarting installation with all dependencies ok")
         rerun_with_anothe_python(os.path.realpath(sys.executable))
+        
     
-class build_sphinx(ori_build_sphinx):
-    '''
-    Build Sphinx documentation in html, epub and man formats 
-    '''
-
-    description = __doc__
-
-    def run(self):
-        self.builder='html'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='epub'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='man'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
     

distutils.ext/obidistutils/core.py

@@ -201,7 +201,5 @@ def setup(**attrs):
     
     if 'ext_modules' not in attrs:
         attrs['ext_modules'] = EXTENTION
-        
-    print "$$$$$$$$$$$$$$$$$$$$$$$$$$$",COMMANDS
-    
+            
     ori_setup(**attrs)

distutils.ext/obidistutils/serenity/.gitignore

@@ -0,0 +1 @@
+/*.pyc

distutils.ext/obidistutils/serenity/pip/.gitignore

@@ -0,0 +1 @@
+/*.pyc

distutils.ext/obidistutils/serenity/pip/_vendor/.gitignore

@@ -0,0 +1 @@
+/*.pyc