Mercurial > repos > siwaa > redelac_stics_t
diff README.md @ 15:af807768332e draft default tip
"planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
| author | siwaa |
|---|---|
| date | Fri, 06 Feb 2026 13:28:00 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Feb 06 13:28:00 2026 +0000 @@ -0,0 +1,34 @@ +## About the redelacSticsTool.bash + +This script is reponsible to set a Stics and SticsRPacks environement and +workspace enabling to launch an virtual experimental plan. + +It has to face that we can't or don't want to modify what is on the container. +This is a prerequisite, for instance when using a container in the Galaxy context. + +### Requirements + +A javastics_path is required to enable Stics. logs, config an plnat subfolder are expected to be found there. + +### What the script does + +note that The Stics binary is used directly from the container. + +1. Create a home folder at the current working directory (the name is not very convenient maybe) +2. Populate with whait is available in the container 3 subfolders logs, config and plant. +3. But remove the config? +4. And populate with the one of the tool, from the galaxy tool folder ( arg 4 ). this could be reconsidered. +5. Populate with a Stics WS given as arg 5 an keep the name. +6. Populate the WS with the csv succession plan given by arg 17. +7. Populate the WS with param_gen.xml and param_newform.xml from the local config. +8. Unzip the climate arg 6 Zip folder and populate the WS with the content AKA stics yearly meteo files +9. Populate USMS, Tec, Ini, Station CSV Files frome args 7 to 10 +10. In Case of specific conf given with arg 11, folder plant is replaced and param_gen and param_newform also +11. Launch the R Script with arg 1 telling to use the optimised facilities of SticsRPacks, arg 2 telling if parallelisation is wanted, arg 3 telling the number of slots, arg 15 giving a scenario name. +12. Zip the result folder to arg 16 +13. If arg 14 zip the WS and give to arg 12 + +### TODO + +Maybe revisiting or simplify the relation between the "base" WS, and the parameters..To provide a generique approach. +For Instance A single parameter = the WS \ No newline at end of file
