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# Script to install CTDConverter and its dependencies via conda
MESSAGE(STATUS "Installing CTDConverter and its dependencies")
MESSAGE(STATUS "Using CTDConverter version @CTDCONVERTER_VERSION@")
MESSAGE(STATUS "Using CTDSchema version @CTDSCHEMA_VERSION@")
# Download Miniconda installer
MESSAGE(STATUS "Installing miniconda")
FILE(DOWNLOAD "https://repo.continuum.io/miniconda/@MINICONDA_INSTALLER@" "@PROJECT_BINARY_DIR@/@MINICONDA_INSTALLER@")
# Install Miniconda
EXECUTE_PROCESS(COMMAND sh @MINICONDA_INSTALLER@ -b -p @MINICONDA_INSTALL_DIR@
OUTPUT_FILE "@LOGFILE_DIR@/miniconda_install_out.log"
ERROR_FILE "@LOGFILE_DIR@/miniconda_install_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
# Install dependencies in the proper order: ctdopts, lxml, ruamel.yaml, downgraded libxml2
# Install CTDopts
MESSAGE(STATUS "Installing CTDopts (CTDConverter dependency)")
EXECUTE_PROCESS(COMMAND "@MINICONDA_INSTALL_DIR@/bin/conda" install -y --channel workflowconversion ctdopts
OUTPUT_FILE "@LOGFILE_DIR@/miniconda_install_ctdopts_out.log"
ERROR_FILE "@LOGFILE_DIR@/miniconda_install_ctdopts_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
# Install Miniconda lxml
MESSAGE(STATUS "Installing lxml (CTDConverter dependency)")
EXECUTE_PROCESS(COMMAND "@MINICONDA_INSTALL_DIR@/bin/conda" install -y lxml
OUTPUT_FILE "@LOGFILE_DIR@/miniconda_install_lxml_out.log"
ERROR_FILE "@LOGFILE_DIR@/miniconda_install_lxml_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
# Install ruamel.yaml
MESSAGE(STATUS "Installing ruamel.yaml (CTDConverter dependency)")
EXECUTE_PROCESS(COMMAND "@MINICONDA_INSTALL_DIR@/bin/conda" install -y --channel conda-forge ruamel.yaml
OUTPUT_FILE "@LOGFILE_DIR@/miniconda_install_ruamel_yaml_out.log"
ERROR_FILE "@LOGFILE_DIR@/miniconda_install_ruamel_yaml_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
# lxml depends on libxml2; installing lxml installs libxml2 v2.9.4., which contains a bug in schema validation
# so, we downgrade to the latest known version of libxml2 that works
MESSAGE(STATUS "Downgrading libxml2 (CTDConverter dependency)")
EXECUTE_PROCESS(COMMAND "@MINICONDA_INSTALL_DIR@/bin/conda" install -y libxml2=2.9.2
OUTPUT_FILE "@LOGFILE_DIR@/miniconda_install_libxml2_out.log"
ERROR_FILE "@LOGFILE_DIR@/miniconda_install_libxml2_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
# Clone CTDConverter
IF(NOT EXISTS "@PROJECT_BINARY_DIR@/CTDConverter")
MESSAGE(STATUS "Cloning CTDConverter GitHub repository")
EXECUTE_PROCESS(COMMAND git clone --branch @CTDCONVERTER_VERSION@ https://github.com/WorkflowConversion/CTDConverter
OUTPUT_FILE "@LOGFILE_DIR@/ctdconverter_clone_out.log"
ERROR_FILE "@LOGFILE_DIR@/ctdconverter_clone_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
ENDIF()
# Clone CTDSchema
IF(NOT EXISTS "@PROJECT_BINARY_DIR@/CTDSchema")
MESSAGE(STATUS "Cloning CTDSchema GitHub repository")
EXECUTE_PROCESS(COMMAND git clone --branch @CTDSCHEMA_VERSION@ https://github.com/WorkflowConversion/CTDSchema
OUTPUT_FILE "@LOGFILE_DIR@/ctdschema_clone_out.log"
ERROR_FILE "@LOGFILE_DIR@/ctdschema_clone_err.log"
WORKING_DIRECTORY @PROJECT_BINARY_DIR@
)
ENDIF()
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