Pipelines Source Instalations

Table of Contents

Source Kit package installation

We strongly recommend to install esoreflex and/or pipelines using one of the package manager methods or the containers, but if necessary, esoreflex and/or pipelines can also be built and installed from source.

Pre-requisites

Please consult the Software Prerequisites page before installing the pipelines or EsoReflex from source.

Please note that for both of the source code based installation methods described below, it is not possible to add pipelines for other instruments, or remove installed pipelines of one or more instruments from an existing installation. If you have an existing pipeline installation and you want a different set of pipelines from what is currently installed, you need to re-do the complete installation procedure as described below selecting all the pipelines you want, and this will result in a complete new installation, in addition to the current one(s), unless of course you remove the current one (see below).

EsoReflex based Pipeline Installations

For an installation of pipeline packages with EsoReflex support please follow the instructions in this section which will install the software in a self-contained, isolated way (making it easy to remove or re-install) and also avoid issues with with other installed software (e.g. *conda).

No Python modules are required during installation, so it is ok if during installation the install script fails to locate all the required python modules. But you will need to either install those required python modules for your system python, or create a (dedicated) python environment for esoreflex and configure esoreflex to use that environment, please see the Using *conda to provide python dependencies for esoreflex knowledgebase article.

  • We recommend that you install the software as follows: bash
    INSTALL_DIR=${HOME}/pipelines/reflex/$(date +%Y-%m-%d)
    mkdir -pv ${INSTALL_DIR}
    cd ${INSTALL_DIR}
    curl -O https://www.eso.org/sci/software/pipelines/install_esoreflex
  • On macOS, if you have used MacPorts to satisfy the Software Prerequisites, do: env -i PATH=/opt/local/bin:$(getconf PATH) bash ./install_esoreflex
  • On macOS, if you have used HomeBrew to satisfy the Software Prerequisites, do: env -i PATH=/opt/local/bin:$(getconf PATH) bash ./install_esoreflex
  • In all other cases do: env -i PATH=$(getconf PATH) bash ./install_esoreflex
  • To completely remove the installation at any time, simply do: rm -fr ${HOME}/pipelines/reflex/<yyyy-mm-dd> where <yyyy-mm-dd> is the date of the pipeline installation you want to remove (assuming it was installed following the above instructions).
  • If you make use of any of these workflows in a scientific publication, please consider citing EsoReflex. You may reference the following paper: Automated Data Reduction Workflows for Astronomy: The ESO Reflex Environment, 2013, Freudling, W., et al., Astron.Astrophys., 559, A96 (Bibtex entry)

Installations without EsoReflex

If you want to install pipelines without EsoReflex support please follow the instruction in this section. It applies to all pipeline packages.

  • bash
    INSTALL_DIR=${HOME}/pipelines/no_reflex/$(date +%Y-%m-%d)
    mkdir -pv ${INSTALL_DIR}/src
    cd ${INSTALL_DIR}/src
    curl -O https://www.eso.org/sci/software/pipelines/install_pipelinekit
  • Download the desired pipeline kit(s) from the Source Kit column in the pipeline table into the <INSTALL_DIR>/src directory.
  • On macOS, if you have used MacPorts to satisfy the Software Prerequisites, back in the terminal in the <INSTALL_DIR>/src directory: env -i PATH=/opt/local/bin:$(getconf PATH) bash ./install_pipelinekit -ignore_gasgano ${INSTALL_DIR} *-kit-*.tar.gz
  • On macOS, if you have used HomeBrew to satisfy the Software Prerequisites, back in the terminal in the <INSTALL_DIR>/src directory: env -i PATH=/opt/local/bin:$(getconf PATH) bash ./install_pipelinekit -ignore_gasgano ${INSTALL_DIR} *-kit-*.tar.gz
  • In all other cases, back in the terminal in the <INSTALL_DIR>/src directory: env -i PATH=$(getconf PATH) bash ./install_pipelinekit -ignore_gasgano ${INSTALL_DIR} *-kit-*.tar.gz
  • After the installation the <INSTALL_DIR>/src directory can be deleted. rm -fr ${INSTALL_DIR}/src
  • To completely remove the installation at any time, simply do: rm -fr ${HOME}/pipelines/no_reflex/<yyyy-mm-dd> where <yyyy-mm-dd> is the date of the pipeline installation you want to remove (assuming it was installed following the above instructions).