Troubleshooting Galaxy Docker -- QIIME2

Hi @sashaphex. I am also having somewhat similar problem but could trivial for many people. My first time to setup a Galaxy Docker Container to work through some of my data by QIIME2. I first created a collection of fastq.gz files. Once I start importing to QIIME2 via Tools and hence to convert to the artifacts-galaxy immediately stops execution. I went back to the container, refreshed/restarted the image( Quay). The galaxy Docker interface created has also some lacking. Eg. it does not show a box to name a history plus there is no way of sharing data or analysis or even creating a workflow. How many million things am I missing? Thank ya’ll for help

Welcome, @Wossen

This is how an anonymous session works in any Galaxy deployment.

Creating an account, and logging into it, will usually expose fuller functionality. Whether that applies to this specific image or not – I’m not sure.

More documentation is here that may help:

If you are still stuck after reviewing, please describe the administrative/account steps you have done so far. I am going to also cross-post your question to this chat (public!). The developers may reply here or there, and feel free to join the chat. You're invited to talk on Matrix.

Hi @jennaj , thanks heaps. Yes anonymity has been a problem I did not realize at first. I managed to import FASTQ files and imported/undertook analysis via QIIME2 tools for few samples (only one by one :)). Uploading via rule-based uploader is appearing to be a challenge as my data has no URL associated to it (uploading locally). I saw in one of your reply/comment to a question that if a file path can be used once tsv file is created to in this thread (Using local files in rule based uploader). I followed those steps: created tsv file with sequence and file path columns. In building rules for uploading condition, I put column A as list identifier, however, “file path” or to that effect is not available for column B (source identifier). Available options are URL, type, etc. I tried in all options…well…expectedly did not work. I know I am all over the place…but if there is any tip, I immensely appreciate it :slight_smile:

Hi @Wossen

There are two ways to apply rules:

  1. During the data upload step.
  • When working at a public Galaxy server, Galaxy will expect the data to be “publicly” available via URL.
  • When running a local server, “public” could mean Galaxy has access/permissions to files within a local network by URL. The data could be behind a firewall eg not exposed to the entire internet but Galaxy needs to be able to “see” and have permissions to copy the data.
  1. After the data is uploaded.
  • The idea is to get data into Galaxy and initially organized in a collection those rules can be applied to.
  • The data needs to contain information in the file names to parse. If not, there is no content to convert into attributes using this method.
  • Sample information can be applied in other ways, explained in that topic.

Just to confuse it more … since you are the admin of the server, you could also load files into Data Libraries (supports file paths with appropriate permissions). You could also set up a Remote Files Directory.

These topics are covered in the Admin GTN tutorials: Galaxy Training!. Cross check those methods with the Galaxy Docker docs since not all steps will be the same: the Galaxy Docker image has some config already implemented and QIMME2 Docker also has some config implemented.