# Error report on dataset import from Galaxy history into Rstudio **URL:** \ **Category:** Uncategorized\ **Tags:** rstudio, gx\_get\ **Created:** [January 17, 2025, 3:27am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470 "2025-01-17T03:27:00Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Jane](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@Jane](https://help.galaxyproject.org/u/Jane)\ **Post date:** [January 17, 2025, 3:27am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470/1 "2025-01-17T03:27:00Z")
Hello everyone, I am trying to import some tsv files from my galaxy history into the Rstudio in [usegalaxy.eu](http://usegalaxy.eu/). I am continuously getting an error message. The command is: > # Get the SNP distance matrix object from Galaxy > > distance ← gx\_get(2) The error report is: DEBUG:root:Host IP determined to be b’172.17.0.1\n’ DEBUG:root:TestURL url=[https://usegalaxy.eu](https://usegalaxy.eu) obj=False DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863 HTTP/1.1” 200 None DEBUG:root:TestURL url=[https://usegalaxy.eu](https://usegalaxy.eu) state=success DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at [https://usegalaxy.eu](https://usegalaxy.eu) history=8b2ff66762999863 dataset=2 DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863/contents HTTP/1.1” 200 None DEBUG:root:Cached, not re-downloading /import/2 Can anyone help? Thanks. ---
**Author:** ![dadrasarmin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dadrasarmin/32/6508_2.png) [@dadrasarmin](https://help.galaxyproject.org/u/dadrasarmin)\ **Post date:** [January 17, 2025, 12:35pm UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470/2 "2025-01-17T12:35:57Z")
Hi, As already mentioned [here](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618/3), the function `gx_get()` just returns a path to a file for you. It does not read a table for you. How can you import your file? Let’s say you want to import your tsv table which is dataset number 7 in your current history as RStudio. You can get the path as follows: ```auto table <- read.table(gx_get(7), header=T, sep="\t", row.names = 1) ``` Of course, you can also do it differently such as: ```auto path <- gx_get(7) table <- read.table(path, header=T, sep="\t", row.names = 1) ``` It is important to understand that `gx_get()` returns just a path and do not transfer any file. Best regards, Armin ---
**Author:** ![Jane](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@Jane](https://help.galaxyproject.org/u/Jane)\ **Post date:** [January 20, 2025, 1:27am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470/3 "2025-01-20T01:27:07Z")
Hi Armin, My tsv file dataset No. is 2. The first command you suggested is still be repoted error as following: table ← read.table(gx\_get(2), header=T, sep=“\t”, row.names = 1) Error is: > table ← read.table(gx\_get(2), header=T, sep=“\t”, row.names = 1) > DEBUG:root:Host IP determined to be b’172.17.0.1\n’ > DEBUG:root:TestURL url=[https://usegalaxy.eu](https://usegalaxy.eu) obj=False > DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) > DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863 HTTP/1.1” 200 None > DEBUG:root:TestURL url=[https://usegalaxy.eu](https://usegalaxy.eu) state=success > DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at [https://usegalaxy.eu](https://usegalaxy.eu) history=8b2ff66762999863 dataset=2 > DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) > DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863/contents HTTP/1.1” 200 None > DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) > DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/datasets/4838ba20a6d8676528b22d02379866c7?hda\_ldda=hda HTTP/1.1” 200 None > DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) > DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863/contents/4838ba20a6d8676528b22d02379866c7/display?to\_ext=tsv HTTP/1.1” 200 173 > /import/2 The second command is also be repoted error as following: path ← gx\_get(2) table ← read.table(path, header=T, sep=“\t”, row.names = 1) The error is: > path ← gx\_get(2) > DEBUG:root:Host IP determined to be b’172.17.0.1\n’ > DEBUG:root:TestURL url=[https://usegalaxy.eu](https://usegalaxy.eu) obj=False > DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) > DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863 HTTP/1.1” 200 None > DEBUG:root:TestURL url=[https://usegalaxy.eu](https://usegalaxy.eu) state=success > DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at [https://usegalaxy.eu](https://usegalaxy.eu) history=8b2ff66762999863 dataset=2 > DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): [usegalaxy.eu:443](http://usegalaxy.eu:443) > DEBUG:urllib3.connectionpool:[https://usegalaxy.eu:443](https://usegalaxy.eu:443) “GET /api/histories/8b2ff66762999863/contents HTTP/1.1” 200 None > DEBUG:root:Cached, not re-downloading > /import/2 > table ← read.table(path, header=T, sep=“\t”, row.names = 1) Can you help me again? Thank you very much Jane ---
**Author:** ![dadrasarmin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dadrasarmin/32/6508_2.png) [@dadrasarmin](https://help.galaxyproject.org/u/dadrasarmin)\ **Post date:** [January 20, 2025, 6:56am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470/4 "2025-01-20T06:56:51Z")
Hi Jane, Could you please share your history with me? Then, I can help better. Best regards, Armin ---
**Author:** ![Jane](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@Jane](https://help.galaxyproject.org/u/Jane)\ **Post date:** [January 20, 2025, 7:13am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470/5 "2025-01-20T07:13:09Z")
Hi Armin, I have shared my history as following link: > **[Galaxy](https://usegalaxy.eu/published/history?id=8b2ff66762999863)** > > Galaxy is a community-driven web-based analysis platform for life science research. And I am trying and excising a pipeline follow the tutorial [Identifying tuberculosis transmission links: from SNPs to transmission clusters]([https://Identifying](https://Identifying) tuberculosis transmission links: from SNPs to transmission clusters) Thank you for your help. Jane ---
**Author:** ![dadrasarmin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dadrasarmin/32/6508_2.png) [@dadrasarmin](https://help.galaxyproject.org/u/dadrasarmin)\ **Post date:** [January 20, 2025, 9:12am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470/6 "2025-01-20T09:12:15Z")
Hi Jane, I tried to import the tsv file from Galaxy to RStudio and it worked (I attached an screenshot.) ![import_table](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/0d6ee0d4473986b4072da3171675a8ad72ed4560.png) I noticed two differences in the code that you shared here. You are using `←` instead of `<-` and `“` instead of `"`. If you copy paste the code from here to your RStudio, please check that these parts are written as R syntax in your code. I hope this solves your problem. Best, Armin