# Can't upload data with gx\_get() in Rstudio tool or install GalaxyConnect into desktop R Studio

**URL:** <https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618>\
**Category:** usegalaxy.eu support\
**Tags:** gtn-tutorial, troubleshooting, rstudio\
**Created:** [January 29, 2024, 11:13pm UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618 "2024-01-29T23:13:38Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![sfer3175](https://avatars.discourse-cdn.com/v4/letter/s/d9b06d/32.png) [@sfer3175](https://help.galaxyproject.org/u/sfer3175)\
**Post date:** [January 29, 2024, 11:13pm UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/1 "2024-01-29T23:13:38Z")

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Hello,

I’m trying to follow [this tutorial](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html) that uses gx\_get() to upload datafiles from my history ([Galaxy](https://usegalaxy.eu/published/history?id=2c5b68e399ec7dd1)) into the RStudio interactive tool. I’ve created multiple histories and restarted the Rstudio tool multiple times and keep getting the same debug error message pictured below.

 ![Screenshot 2024-01-29 at 4.54.43 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/4/4a9e36a3051312b58305c7263a7d3bca0d30cdb6.jpeg)

Even thought the import 1 ect message will pop up, no data files are being imported as far as I can tell.  
I tried to switch to using my desktop R studio and cannot get Galaxy Connector to install there to use gx\_get(). I also get an error message that the package has a non zero exit.

I’ve seen others with this problem on the forum but a solution has not been posted.

Any idea why this is happening? I could not get the Rstudio tool to launch on the [usegalaxy.org](http://usegalaxy.org) site at all. I’m not sure if that’s related.

-Thanks for your help!  
Sarah

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 1, 2024, 12:36am UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/2 "2024-02-01T00:36:25Z")

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Welcome, @sfer3175

I can reproduce the launching issue at [UseGalaxy.org](http://UseGalaxy.org) and opened a ticket for the fix here: [Rstudio fails to launch at ORG · Issue #681 · galaxyproject/usegalaxy-tools · GitHub](https://github.com/galaxyproject/usegalaxy-tools/issues/681)

For a local configuration, let’s get some help with the Galaxy Connector at the developers chat. They may reply here or there, and you are welcome to join the chat tool! [You're invited to talk on Matrix](https://matrix.to/#/!fVQwotRzniGGJbeUUi:gitter.im/$upApi4aTVnTeocmcQXi_SeONZlgyUfos5O6DHToaBRk?via=gitter.im&via=matrix.org)

Updated: See solution reply instead. ~~When I tried using Rstudio at [UseGalaxy.eu](http://UseGalaxy.eu) directly, the gx\_get() function failed the same way your query did, so the problem seems to be with Galaxy Connector. The developers can help us to confirm. Also going to ping a few of them here in case I missed something else~~: @wm75 @bernt-matthias

Thanks for reporting the problem!

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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [February 1, 2024, 11:07am UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/3 "2024-02-01T11:07:23Z")

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> Even thought the import 1 ect message will pop up, no data files are being imported as far as I can tell.

There isn’t anything wrong here, but you need to assign the return value to some variable to be able to work with it, e.g.,

`my_data <- gx_get(2)`

Note: `gx_get()` makes the specified data available inside RStudio, but what’s returned by it is just a path to the data, for example the string `"/import/2"`.

With this path you can then read from the resource with R functions that you’d normally use to read your input, e.g., if your data is tabular you could do sth like:

`read.table(my_data, header=T, sep="\t", row.names = 1)`

which in this case is equivalent to:

`read.table("/import/2", header=T, sep="\t", row.names = 1)`

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 1, 2024, 5:28pm UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/4 "2024-02-01T17:28:13Z")

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Thanks @wm75

For some reason I always forget that the data isn’t moved directly into the environment with gx\_get()! I expect it to work like gx\_put() in the reverse. Maybe we need another variable … something like gx\_fetch(). I’ll propose an enhancement.

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**Author:** ![sfer3175](https://avatars.discourse-cdn.com/v4/letter/s/d9b06d/32.png) [@sfer3175](https://help.galaxyproject.org/u/sfer3175)\
**Post date:** [February 1, 2024, 6:42pm UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/5 "2024-02-01T18:42:48Z")

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Thank you so much! I was totally stuck and was missing this info.

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 23, 2024, 5:47pm UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/6 "2024-02-23T17:47:16Z")

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> [@jennaj](#):
>
> I can reproduce the launching issue at [UseGalaxy.org](http://UseGalaxy.org) and opened a ticket for the fix here: [Rstudio fails to launch at ORG · Issue #681 · galaxyproject/usegalaxy-tools · GitHub](https://github.com/galaxyproject/usegalaxy-tools/issues/681)

**Rsutdio** is available at [UseGalaxy.org](http://UseGalaxy.org) as of later yesterday. Thanks for all who reported the problem, and who fixed it up!