Error report on dataset import from Galaxy history into Rstudio

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1

Hello everyone,
I am trying to import some tsv files from my galaxy history into the Rstudio in 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 obj=False
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 “GET /api/histories/8b2ff66762999863 HTTP/1.1” 200 None
DEBUG:root:TestURL url=https://usegalaxy.eu state=success
DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at https://usegalaxy.eu history=8b2ff66762999863 dataset=2
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool: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.

2

Hi,

As already mentioned here, 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:

table <- read.table(gx_get(7), header=T, sep="\t", row.names = 1)

Of course, you can also do it differently such as:

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

3

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 obj=False
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 “GET /api/histories/8b2ff66762999863 HTTP/1.1” 200 None
DEBUG:root:TestURL url=https://usegalaxy.eu state=success
DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at https://usegalaxy.eu history=8b2ff66762999863 dataset=2
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool: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
DEBUG:urllib3.connectionpool: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
DEBUG:urllib3.connectionpool: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 obj=False
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 “GET /api/histories/8b2ff66762999863 HTTP/1.1” 200 None
DEBUG:root:TestURL url=https://usegalaxy.eu state=success
DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at https://usegalaxy.eu history=8b2ff66762999863 dataset=2
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool: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

4

Hi Jane,

Could you please share your history with me? Then, I can help better.

Best regards,

Armin

5

Hi Armin,
I have shared my history as following link:

And I am trying and excising a pipeline follow the tutorial [Identifying tuberculosis transmission links: from SNPs to transmission clusters](https://Identifying tuberculosis transmission links: from SNPs to transmission clusters)

Thank you for your help.
Jane

6

Hi Jane,

I tried to import the tsv file from Galaxy to RStudio and it worked (I attached an screenshot.)

import_table
import_table1912×1068 237 KB

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

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