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Yvan Le Bras
@yvanlebras
so here is the code wonder Björn
Marie Jossé
@Marie59
cp  L2A_T38QKM_A035839_20220503T074203_Refl && cp /tmp/tmp44kveofp/files/000/dataset_138.dat L2A_T38QKM_A035839_20220503T074203_Refl.hdr && Rscript '/home/pndb-cr/Documents/GitHub/Data_explo_tools/test_planemo/data_reading.r' 'L2A_T38QKM_A035839_20220503T074203_Refl' 'L2A_T38QKM_A035839_20220503T074203_Refl.hdr' '/tmp/tmp44kveofp/files/000/dataset_255.dat' '/tmp/tmp44kveofp/files/000/dataset_256.dat' '/tmp/tmp44kveofp/files/000/dataset_257.dat' '<galaxy.tools.wrappers.DatasetCollectionWrapper object at 0x7f5e027c4790>'
Yvan Le Bras
@yvanlebras
and here is the stdout from Galaxy side
where we don't have the file /tmp.... for L2A_T38QKM_A035839_20220503T074203_Reflelement_identifier
when the file in input_raster is binary
BUT when this is not a binary file BUT a txt one (in input_raster)
:
(roulement de tambour ;) )
Marie Jossé
@Marie59
cp /tmp/tmp44kveofp/files/000/dataset_130.dat S2A_Subset.hdr && cp /tmp/tmp44kveofp/files/000/dataset_138.dat L2A_T38QKM_A035839_20220503T074203_Refl.hdr && Rscript '/home/pndb-cr/Documents/GitHub/Data_explo_tools/test_planemo/data_reading.r' 'S2A_Subset.hdr' 'L2A_T38QKM_A035839_20220503T074203_Refl.hdr' '/tmp/tmp44kveofp/files/000/dataset_258.dat' '/tmp/tmp44kveofp/files/000/dataset_259.dat' '/tmp/tmp44kveofp/files/000/dataset_260.dat' '<galaxy.tools.wrappers.DatasetCollectionWrapper object at 0x7f5e020742d0>'
bgruening
@bgruening:matrix.org
[m]
you test this with planemo test
or planemo serve?
single-quotes are missing around the filenames?
What kind of format is that?
Yvan Le Bras
@yvanlebras
but this work "fine" with txt file
planemo serve
bgruening
@bgruening:matrix.org
[m]
yes, its strange
Yvan Le Bras
@yvanlebras
hey hey ;)
bgruening
@bgruening:matrix.org
[m]
can you see the binary as uploaded file in Galaxy, with filesize and a path?
Yvan Le Bras
@yvanlebras
I think we will try to add the datatype to see
name and filesize are ok
path is not an info of the "dataset information" isn't it ?
bgruening
@bgruening:matrix.org
[m]
it is but only for admins I think
Yvan Le Bras
@yvanlebras
she is
Can we test the creation of a datatype using planemo ???
bgruening
@bgruening:matrix.org
[m]
if you use a local galaxy instance, for example with planemo test --galaxy_root /home/yvan/galaxy
you can simply add the datatype to this local galaxy instance
Yvan Le Bras
@yvanlebras
ok
bgruening
@bgruening:matrix.org
[m]
e.g. by editing the datatypes_conf.xml file
Yvan Le Bras
@yvanlebras
ok
but here we just launch planemo serve so we can't directly add a datatype ?
(but we can launch a Galaxy instance with planemo test as you propose ;) )
bgruening
@bgruening:matrix.org
[m]
if you use planemo serve --galaxy_root /home/yvan/galaxy
it will use this Galaxy with your local modifications
https://planemo.readthedocs.io/en/latest/configuration.html?highlight=galaxy_root#configuration
https://planemo.readthedocs.io/en/latest/commands/serve.html?highlight=galaxy_root#serve-command
Yvan Le Bras
@yvanlebras
and to be sure ;) we can't make "just" a planemo serve with a datatypes_conf.xml file aside our xml tool file so planemo ""understand"" we want to test a new datatype ?
bgruening
@bgruening:matrix.org
[m]
not that I know ... but you should really have a local Galaxy checkout if you are running planemo
I would recommend it that way
Yvan Le Bras
@yvanlebras
right! Agree !!!!
Yvan Le Bras
@yvanlebras
Hi everyone
Hope all is ok
for you all !
I confirm, now we have added the binary datatype, we can see the PATH to the binary file on the stdout
Anton Nekrutenko
@nekruten:matrix.org
[m]
@yvanlebras: -> are you in Paris by any chance next week?
Yvan Le Bras
@yvanlebras
oh oh @nekruten:matrix.org you have some chance, I will be in Paris monday evening (from 9pm Montparnasse) and completely free until tuesday morning! An idea about a restaurant and / or night club ? ;)
3 replies
bgruening
@bgruening:matrix.org
[m]
Anton Nekrutenko: just talked to ena people here.
The webinterface is not working but the data is there
Try FTP?
Anton Nekrutenko
@nekruten:matrix.org
[m]
ok
Anton Nekrutenko
@nekruten:matrix.org
[m]
late july?
2 replies