Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Yvan Le Bras
@yvanlebras
;) sorry for the not precise questoin ;)
in the command line (when with planemo we execute the tool, then look at the job "information" and the "command line"), we have "nothing" where we put the $input (name of the input parameter)
when the file is binary
when the fle is txt, we have for example input_file.txt
bgruening
@bgruening:matrix.org
[m]
mh, that sounds strange
can you point us to some code?
Yvan Le Bras
@yvanlebras
maybe a security thing for binary files who are not specified in the Galaxy datatypes ?
Marie Jossé
@Marie59
cp $input_raster ${input_raster.element_identifier} &&
        cp $input_header ${input_header.element_identifier} &&
        Rscript
            '$__tool_directory__/data_reading.r'
            '$input_raster.element_identifier'
            '$input_header.element_identifier'
            '$output_shannon'
            '$output_alpha'
            '$output_beta'
            '$plots'
        ]]>
    </command>
    <inputs>
        <param name="input_raster" type="data" format="binary,txt" label="Input raster"/>
        <param name="input_header" type="data" format="txt" label="Input raster header"/>
    </inputs>
Yvan Le Bras
@yvanlebras
Thjank you MArie for copy pasting the xml code ;)
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