Merge pull request #116 from helenkirk/casa5

Casa5

science-containers/Dockerfiles/casa/version-5.0-5.8/Dockerfile

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+FROM images.canfar.net/skaha/centos:6.10
+#NB: 6.10 version is needed (rather than generic 6) to get UVMultiFit package
+# dependencies to install properly via yum
+
+#final sets of package installations: As of Aug 22/24, cannot re-build
+# centos6.10 base container from source
+
+#Admit & analysisUtils packages, respectively:
+RUN yum install -y tcsh wget && \
+#additional packages for UVmultifit
+    yum install -y gcc gcc-c++ gsl-devel fftw-devel git.x86_64
+
+# setup all required env variables
+ARG CASA_RELEASE
+ENV CASA_RELEASE=${CASA_RELEASE}
+ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/casa/bin
+
+# untar casa databundle to container
+ADD ${CASA_RELEASE}.tar.gz /opt/
+
+# chown because the untarred casa has wrong owner/group
+RUN chown -R root:root /opt/${CASA_RELEASE} && ln -s /opt/${CASA_RELEASE} /opt/casa
+
+
+# add the admit enhancement (issue #25)
+RUN mkdir /opt/admit
+ADD admit /opt/admit
+RUN cd /opt/admit && \
+    autoconf && ./configure --with-casa-root=/opt/${CASA_RELEASE}
+
+# Allow runtime symlink creation to the casa-data-repository
+# Create a dangling symlink to casa-data-repository so that after deployment
+# the symlink will link to the actual casa-data-repository in storage.
+RUN mkdir -p /arc/projects/casa-data-repository && \
+    rm -rf /opt/${CASA_RELEASE}/data && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE}/data && \
+    chmod 777 /opt/${CASA_RELEASE} && \
+    rm -rf /arc && \
+#
+    mkdir /skaha
+ADD init.sh /skaha/
+
+# generate missing dbus uuid (issue #47)
+RUN dbus-uuidgen --ensure
+
+ADD nsswitch.conf /etc/
+
+#install UVMultiFit from github.  Recommended location for install as below
+#user imports into casa after initiating a session by typing 
+# 'from NordicARC import uvmultifit as uvm'
+RUN mkdir /opt/casa/NordicARC && \
+#(NB: this link is for the 'master' branch which does the python2 version)
+    cd /opt/casa/NordicARC && \
+    git clone https://github.com/onsala-space-observatory/UVMultiFit.git && \
+#now update the CASA path within the Makefile, in a somewhat clunky way
+    cd /opt/casa/NordicARC/UVMultiFit && \
+    echo "CASADIR="/opt/${CASA_RELEASE} >> casadir.txt && \
+    cat casadir.txt Makefile >> Makefile2 && \
+    cd /opt/casa/NordicARC/UVMultiFit && \
+    mv Makefile2 Makefile && rm -f casadir.txt && \
+#run the installation script
+    cd /opt/casa/NordicARC/UVMultiFit && make install && \
+#-----------------
+#One final note relevant for users: the recommended install tests expect
+# the tests to be run in the program directory, where users will not
+# have write access in our containers.  One easy solution is to copy the
+# relevant directories from /UVMultiFit into a user's directory and then 
+# run the tests there.
+#
+#have the UVMultiFit import instructions echoed to terminal start-up
+    echo 'cat /etc/motd' >> /etc/profile.d/motd.sh && \
+    echo 'To load the UVMultiFit package, initiate casa then type "from NordicARC import uvmultifit as uvm"' >> /etc/motd && \
+#
+#Add in analysisUtils package
+    mkdir /opt/casa/analysisUtils  && \
+    cd /opt/casa/analysisUtils && \ 
+    wget ftp://ftp.cv.nrao.edu/pub/casaguides/analysis_scripts.tar && \
+    tar -xvf analysis_scripts.tar 
+#(if above doesn't work, can manually download the package and add as below)
+#ADD ./analysis_scripts.tar /opt/casa/analysisUtils/
+#NB: the analysisUtils path is added to the CASA startup file in the init.sh script
+# (needs access to user's $HOME)
+
+
+RUN cd /opt/${CASA_RELEASE}
+
+CMD [ "/skaha/init.sh" ]

science-containers/Dockerfiles/casa/version-5.0-5.8/Makefile

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+VERSIONS = \
+#	5.0.0-218.el6 #\
+#	5.1.0-74.el6 #\
+#	5.1.1-5.el6 #\
+#	5.1.2-4.el6 #\
+#	5.3.0-143.el6 #\
+#	5.4.0-70.el6 #\ 
+#	5.4.1-32.el6  #\
+#	5.4.2-8.el6  #\
+#	5.5.0-149.el6 #\
+#	5.6.0-60.el6 #\ 
+#	5.7.0-134.el6 #\
+#	5.7.2-4.el6 #\
+#	5.8.0-109.el6 
+
+
+VERSIONS_PIPELINE = \
+#	5.6.1-8.el6
+#	5.6.2-6.el6 #NB: not used in ALMA operations, no longer on CANFAR
+#	5.6.3-19.el6 #NB: not used in ALMA operations, no longer on CANFAR
+
+
+DOCKER_REPO_BASE=images.canfar.net/casa-5/casa
+
+.PHONY: build clean run 
+
+all: build build-pipeline
+
+build: 
+	@- $(foreach V,$(VERSIONS), \
+                ./download.sh casa-release-$(V) current ; \
+                docker build --build-arg CASA_RELEASE=casa-release-$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+build-pipeline: 
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                ./download.sh casa-pipeline-release-$(V) pipeline ; \
+                docker build --build-arg CASA_RELEASE=casa-pipeline-release-$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+
+clean:
+	@- $(foreach V,$(VERSIONS), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean-pipeline:
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+
+clean-all: clean clean-pipeline
+
+
+upload: build
+	@- $(foreach V,$(VERSIONS), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload-pipeline: build-pipeline
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+
+upload-all: upload upload-pipeline