Question: Getting FTP uploaded files into the history of a local Galaxy
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gravatar for Joachim.Berger
7 months ago by
Joachim.Berger40 wrote:

Hi, according to the upload tutorial, files uploaded by FTP can be transferred into the history by clicking the upload symbol, which triggers a new window "Download from web or upload from disk". In this window the files can be transferred via the "choose FTP file" button. However, in the window that I get, there is no such button (see attached image). How can I get the file that I uploaded via FileZilla into the history? Many thanks for suggestions/help. enter image description here

admin ftp config local galaxy • 420 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by Joachim.Berger40

https://ibb.co/n7Cit7

ADD REPLYlink modified 7 months ago • written 7 months ago by Joachim.Berger40
2
gravatar for valdirbarth
7 months ago by
valdirbarth60
valdirbarth60 wrote:

hi joe,

I suppose you are running Galaxy on a server that is not yours, correct? If so, the admin of the server is the one who is supposed to open the galaxy.ini (in the galaxy/config folder) file in the server and edit it to allow FTP uploads. If you do not have access to the file system of the server, I am afraid you'll have to contact someone who has admin privileges.

ADD COMMENTlink written 7 months ago by valdirbarth60

https://galaxyproject.org/admin/config/#ftp

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
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gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

It looks as if FTP needs to be configured on your local Galaxy server. All admin docs are covered in this prior post:

To find docs/FAQs specifically related to FTP configuration, see:

To search all resources, including prior QA about the topic (for troubleshooting config), use this Galaxy Hub search. I used the keywords "ftp" and "local" in this example:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
0
gravatar for Joachim.Berger
7 months ago by
Joachim.Berger40 wrote:

Hi Jen, thank you very much for your answer and efforts, however, I have no idea what you mean. Sorry, but I am a molecular biologist, not a bioinformatician. Though I was able to generate a .vcf file of my mutant with bam/samtools and MiModD, this took me 2 weeks and I am only a beginner when it comes to command line usage.

I have tried to follow the links and ended up at the doc "Galaxy FTP Uploads". Here it is said that "To allow users to upload files to Galaxy via FTP, you'll need to configure Galaxy and install an FTP server. After everything is configured users will be able to upload their files through the FTP server and then select them for importing in the upload dialog in Galaxy. For help with uploading data via FTP on Galaxy Main, please see this tutorial." In this tutorial, however, the button "choose FTP file" is used to upload files into the history. But this is the button that I do not see (attached image). I can't find help with configuring Galaxy.

Similarly, the section "Configure Galaxy" does not make sense to me. "The first step is to choose a directory into which your users will upload files." I don't see/know here to choose from. "Preferably this will be on the same filesystem as Galaxy's datasets (by default, galaxy_dist/database/files/)." Where is this path? "This directory should be set in the config file (galaxy.yml) as ftp_upload_dir." Which config file in which program? The galaxy server, FileZilla etc.? "In the config file, you'll also want to set ftp_upload_site to the hostname your users should connect to via FTP." How? "This will be provided in the help text on the Upload File form." But isn't this "Configure Galaxy" doc that I am ready not already the "Upload File" forum?

Is there a documentation/help that could be used by a beginner/non-informatician? Again, sorry for my incomprehension. Thanks, Joe.

ADD COMMENTlink written 7 months ago by Joachim.Berger40
0
gravatar for Joachim.Berger
7 months ago by
Joachim.Berger40 wrote:

Hi valdirbarth, that makes sense. Thank you very much for your help. I'll contact the server administrator. Joe

ADD COMMENTlink written 7 months ago by Joachim.Berger40
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