Mercurial > repos > siwaa > redelac_stics_t

annotate README.md @ 15:af807768332e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
author siwaa
date Fri, 06 Feb 2026 13:28:00 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
1 ## About the redelacSticsTool.bash
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
2
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
3 This script is reponsible to set a Stics and SticsRPacks environement and
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
4 workspace enabling to launch an virtual experimental plan.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
5
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
6 It has to face that we can't or don't want to modify what is on the container.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
7 This is a prerequisite, for instance when using a container in the Galaxy context.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
8
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
9 ### Requirements
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
10
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
11 A javastics_path is required to enable Stics. logs, config an plnat subfolder are expected to be found there.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
12
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
13 ### What the script does
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
14
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
15 note that The Stics binary is used directly from the container.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
16
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
17 1. Create a home folder at the current working directory (the name is not very convenient maybe)
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
18 2. Populate with whait is available in the container 3 subfolders logs, config and plant.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
19 3. But remove the config?
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
20 4. And populate with the one of the tool, from the galaxy tool folder ( arg 4 ). this could be reconsidered.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
21 5. Populate with a Stics WS given as arg 5 an keep the name.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
22 6. Populate the WS with the csv succession plan given by arg 17.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
23 7. Populate the WS with param_gen.xml and param_newform.xml from the local config.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
24 8. Unzip the climate arg 6 Zip folder and populate the WS with the content AKA stics yearly meteo files
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
25 9. Populate USMS, Tec, Ini, Station CSV Files frome args 7 to 10
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
26 10. In Case of specific conf given with arg 11, folder plant is replaced and param_gen and param_newform also
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
27 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.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
28 12. Zip the result folder to arg 16
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
29 13. If arg 14 zip the WS and give to arg 12
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
30
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
31 ### TODO
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
32
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
33 Maybe revisiting or simplify the relation between the "base" WS, and the parameters..To provide a generique approach.
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents:
diff changeset
34 For Instance A single parameter = the WS