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eso_pipelines

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eso_pipelines [2025/04/04 12:32] – created janseneso_pipelines [2025/04/11 13:54] (current) – jansen
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 ====== ESO pipelines ====== ====== ESO pipelines ======
  
-ESO offers pipeline software for their instruments (see [[https://www.eso.org/sci/software/pipelines/&ved=2ahUKEwikhq2NsL6MAxWGlP0HHf9AKm8QFnoECBoQAQ&usg=AOvVaw0KsrqFAEZvYSHXNaiFfFpj]])+ESO offers pipeline software for their instruments (see [[https://www.eso.org/sci/software/pipelines/]])
 However, installing this software directly on to the system, is usually not possible, since they don't support every version of Fedora or RedHat. However, installing this software directly on to the system, is usually not possible, since they don't support every version of Fedora or RedHat.
  
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 There are however a couple of drawbacks: if will be less efficient with cp, memory and disk space, and you may have to pass some additional options to bypass parts of the isolation, in order to make data available to programs running in the container. There are however a couple of drawbacks: if will be less efficient with cp, memory and disk space, and you may have to pass some additional options to bypass parts of the isolation, in order to make data available to programs running in the container.
  
-ESO's site about apptainer has some more information about usage and options, see [[https://www.eso.org/sci/software/apptainer.html+We currently have a couple of apptainers in ''/software/eso'', the one called ''pipelines.sif'' has a large selection of pipelines (see below). To load the apptainer and start a command from it: 
 +  apptainer exec /software/eso/pipelines.sif [command] 
 +e.g. 
 +  apptainer exec /software/eso/pipelines.sif esoreflex molecfit
  
 +The apptainer always makes the current directory and the user's home available to commands running inside it. If you need access to data in other directories, these can be ''bound'' to the apptainer to make them available:
 +  apptainer exec --bind /my/data/dir:/data /software/eso/pipelines.sif esoreflex
 +This binds ''/my/data/dir'' on the real system to a path ''/data'' inside the apptainer. Or:
 +  apptainer exec --bind /almastorage /software/eso/pipelines.sif esoreflex
 +to make all of the disk ''/almastorage'' visible in the container, under that same name (of course the app will still only have access to data where the user has access).
  
 +
 +ESO's site about apptainer has some more information about usage and options, see [[https://www.eso.org/sci/software/apptainer.html]] (skip the part about installation if you run on Sterrewacht workstations, that has already been done for you)
 +
 +===== Available pipelines =====
 +At the moment , the following pipelines are available in ''/software/eso/pipelines.sif'':
 +| cr2re | efosc |eris | esotk |
 +| espda | espdr | fors| giraf |
 +| gravity | harps | hawki | iiinstrument|
 +| kmos |matisse | molecfit | muse|
 +| nirps | sinfo | spher | uves| 
 +| vcam| vimos | visir | xshoo |
 +Refer to the ESO documentation about startup methods, options, required parameters etc.
eso_pipelines.1743769956.txt.gz · Last modified: by jansen

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