docker: invalid reference format mac
I hope mean clear to you and this will solve your issue asap. You can get around this by passing an empty file to blobtools add, which will label everything as no-hit: The newer image (1.3.2) was pulled but I am still getting a taxdump error with the first command: docker run -it --rm --name btk -u $UID:$groups -v /Users/amcdonnell/Analyses/blobtools/datasets:/blobtoolkit/datasets -v /Users/amcdonnell/Analyses/blobtools/membranacea.contigs.tab.edited.fasta:/blobtoolkit/data genomehubs/blobtoolkit:latest ./blobtools2/blobtools create --fasta /blobtoolkit/datasets/membranacea.contigs.tab.edited.fasta --taxid 1234 --taxdump databases/ncbi_taxdump /blobtoolkit/datasets/membranacea_dataset. ValueError: min() arg is an empty sequence. Does this part take a while? Using this through Docker is just not intuitive to me, I think. It turned out to be. I've retagged latest so it is now the most up to date, but if you use genomehubs/blobtoolkit:1.3.2 in your command instead of genomehubs/blobtoolkit:latest it will definitely use that version. To confirm, is this the docker command you are running? Did you remember to change ~/.n8n to a Windows path? Parsing taxdump ERROR: You may need to rebuild the BlobDir to run this command. I have the file membranacea.contigs.fasta (almost 1.2 GB, so not empty) in /Users/amcdonnell/Analyses/blobtools/datasets, amcdonnell$ docker run -it --rm --name btk -u $UID:$groups -v /Users/amcdonnell/Analyses/blobtools/datasets:/blobtoolkit/datasets -v /Users/amcdonnell/Analyses/blobtools/membranacea.contigs.fasta:/blobtoolkit/data genomehubs/blobtoolkit:latest ./blobtools2/blobtools create --fasta /blobtoolkit/data/membranacea.contigs.fasta --taxid 1234 --taxdump taxdump /blobtoolkit/datasets/membranacea_dataset Really. Sorry to hear this still isn't working. ERROR: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp. I tried to run the blobtools view command in docker to see where you may have gone wrong but although I didn't hit the same error, I couldn't see any output files on my local filesystem even after the command appeared to run successfully so I'll need to debug that but am currently unsure where to start. I've updated the image (1.3.2) with the tax dump restored and tested a few commands that should hopefully help you get some plots out this time. Tried pulling down the latest version of n8n, seemed to do so successfully, though I dont know where its pulling to. Trying to get n8n up and running with Docker Desktop for Windows. I suspect there is probably a windows version of ~ maybe something like %HOME% or $HOME but it might be easier to just manually set a path and see what happens. No problem! Traceback (most recent call last): waiting for element snail_save_png` Already on GitHub? Any help/guidance for a newby? See docker run --help. to your account. Thanks so much again. privacy statement. and taxid? docker run -it -v $(pwd):/app -p 5005:5005 --net action-link rasa/rasa:2.8.2 shell. I'm not sure what nodes.dmp is or what it should come from should I provide a file for taxdump? This looks like a problem with the PYTHONPATH variable. I used the docker run command as above with both --taxdump taxdump and --taxdump databases/ncbi_taxdump. I've not seen that error before so don't know what is causing it. waiting for element cumulative_save_png. Sorry if I wasn't very clear last time. Here's what I'm entering: I've tried editing the above in various ways including deleting the -u part (I suspect I don't need it, but I don't really know). docker pull genomehubs/blobtoolkit:1.3.2 1.3.2: Pulling from genomehubs/blobtoolkit Digest: sha256:0a81055d1ba4fcdd918c549355419718abef00b8c4771d9cc87be17bfff91e02 Status: Image is up to date for genomehubs/blobtoolkit:1.3.2 docker.io/genomehubs/blobtoolkit:1.3.2. Fetching membranacea_dataset.cumulative.png docker run -it --rm --name n8n -p 5678:5678 -v C:/Users/brpw/.n8n:/home/node/.n8n n8nio/n8n. docker run -it -v ~/dataset:/dataset -v ~/inference:/inference -v ~/result:/result floydhub/pytorch:0.4.0-py2.29/inference/inference.sh, http://challenge.xfyun.cn/aicompetition/techDetail. The new container can run the entire pipeline without creating additional conda environments (though including all the dependencies has made it rather large). - processing tig00030305=37045=1suggestBubble=noCircular=no: : 2122it [00:55, 38.16it/s] Parsing taxdump ERROR: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp. Hi again! Run blobtools create with genomehubs/blobtoolkit:1.3.2 so --taxdump databases/ncbi_taxdump will work: Start up the Viewer with ports bound so you have the option of opening it up in a browser: Use docker exec to run blobtools view to get a snail plot: This will show an error when it tries to stop the viewer that is controlled by a different process bu this happens after the plot is generated so can be ignored: Alternatively omit the --host option and it will spin up a new viewer instance inside the container for this one command. docker: invalid reference format. localhost didn't send any data. When I swapped in the 1.3.2 it worked! Once Ive downloaded the official image from Docker (or pulled it using CMD), where would I find it? \Program \program, Powered by Discourse, best viewed with JavaScript enabled. $(pwd) present working directory on which you are working. I tried that, and get the same error any other suggestions? ModuleNotFoundError: No module named 'docopt'. are not shared from OS X and are not known to Docker. File "/blobtoolkit/blobtools2/lib/add.py", line 165, in from docopt import docopt I can't reproduce that with the latest container versions (1.3.2 or a 1.3.3 version that I uploaded today) so I'm not sure what to suggest. That's odd, the view command getting stuck at that point suggests it is not able to connect to the Viewer being hosted in the container. docker run -it --rm --name n8n -p 5678:5678 -v ~/.n8n:/home/node/.n8n n8nio/n8n. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. (base) mac-amcdonnell-p:blobtools amcdonnell$ docker exec -it btk \. ok, it looks like that worked! Bullying newbies! Fetching membranacea_dataset.cumulative.png It worked. Loading sequences from /blobtoolkit/datasets/membranacea.contigs.tab.edited.fasta, Then I ran Hi again, The notes swap between singularity and docker as it can run in either - let me know if you want any examples translated from one to the other. ERR_EMPTY_RESPONSE"). It turned out to be. docker run -it -v D:\Program Files\RASA\myproject-2\rasa-x-waapi\myenv\Docker:/app -p 5005:5005 --net my-project-2 rasa/rasa:2.8.2 shell. Thanks for letting me know about taxdump. ERROR: 'identifiers.json' was not found in the BlobDir. Does that need to be corrected on your end or mine? Are you getting the same error message? I figured out what was wrong and fixed it. I'll look it up, too but I wanted to update. Powered by Discourse, best viewed with JavaScript enabled. Traceback (most recent call last): docker exec -it btk ./blobtools2/blobtools view --host http://localhost:8080 --out output --view cumulative membranacea_dataset, output to screen, stays stuck here Try using / or \\ instead of \. OR you just running the docker on port 5005? If you are running docker on a remote server, you can forward the ports over ssh by connecting with something like ssh -L 8080:localhost:8080 -L 8000:localhost:8000 username@remote_server, then you can connect as if it was running locally with the link above. (should bee at the same level as the -u and -v options) I can try to find a more robust solution once I know if that works. You could try viewing the plots interactively in a web browser outside the container if you bind ports for the API and client when starting the btk container, so: start the container again with bound ports: then view the plots in a browser by visiting http://localhost:8080/view#Datasets. Now I'm getting another error about an empty file. Here is what I'm doing and what I'm getting out. I tried to run Maybe I'm missing some code? I keep getting the error: Any suggestions on what I could do differently to get this software to run? Tried running your code; got the following response: This is after making the folder C:/Users/n8n/. then lots of tigs get processed, output to screen ends with: There's some notes on the new version in a github gist that may be useful. Have a question about this project? I've been running this through docker locally and still can't get any plots to appear, through any browser, even after following your above advice (I get this: "This page isn't working. See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info. I'm having trouble working out where the problem is so I can't suggest an immediate fix. Copied from the website, So this incident tells us that as a publisher, we must use. ModuleNotFoundError: No module named 'docopt'. File "/blobtoolkit/blobtools2/lib/add.py", line 132, in main You signed in with another tab or window. Loading http://localhost:8080/view/dataset/membranacea_dataset/cumulative?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg 8b3c47dbcaf798de734b8954496aa4c676e9e54a96b36a1bb268c446c6ad1fe9, then I ran this to make a plot You can put whatever you want really just make sure it is a local path, I suspect the issue is where ~ is a shortcut on Mac / Linux systems for the current users home directory so assuming your windows logon name is BRPW the command below should just work. I'm new to docker, so thanks for the explanation. Still beginning my journey into the world of code/programming. to check that it is able to find the Viewer. . By default commands in the container run in a /blobtoolkit directory that already contains blobtools2, data and datasets subdirectories so it's easiest to bind to these. main() Still hasnt worked, Im afraid. Tried all lower-case. For clarity, I tried using my normal user folder (my full name with capitals), but got this: Try using your normal user folder but lowercase it all so maybe c:\users\ben\.n8n if that doesnt do it I can set up a Windows virtual machine and give it a quick bash and see what happens. Hey again! Any chance you send over the full command you are running or DM it if you want. I just checked and the latest image tag was still pointing to 1.3.1 so the tax dump issue was still there. So something like: docker run -it --rm --name n8n -p 5678:5678 -v C:/Users/Username/.n8n:/home/node/.n8n n8nio/n8n. Traceback (most recent call last): A backslash usually means a special character is next (like \n for Enter and \\ for \): @jennoi are you making a bridge/network between rasa and rasa-sdk (action server) while using --net ? Sign in (base) mac-amcdonnell-p:blobtools amcdonnell$ touch output/blank.hits.out ERROR: Unable to parse /blobtoolkit/taxdump/nodes.dmp. This step should run quite quickly so there is clearly something not working as expected. docker run -it --rm --name btk -u $UID:$groups -v /Users/amcdonnell/Analyses/blobtools/datasets:/blobtoolkit/datasets -v /Users/amcdonnell/Analyses/blobtools/membranacea.contigs.tab.edited.fasta:/blobtoolkit/data genomehubs/blobtoolkit:latest ./blobtools2/blobtools create --fasta /blobtoolkit/datasets/membranacea.contigs.tab.edited.fasta --taxid 1234 --taxdump databases/ncbi_taxdump /blobtoolkit/datasets/membranacea_dataset, output to screen Perhaps I didn't incorporate your suggestion correctly? but I got error Good Luck! I'm now trying to generate plots and getting stopped by a "waiting for element cumulative_save_png" or "waiting for element snail_save_png" and I'm not sure what to do with it or how long to let it sit. After removing container, I ran: The culprit: http://challenge.xfyun.cn/aicompetition/techDetail, Then replace it with the normal half-width symbol, Reference : https://blog.csdn.net/weixin_33856370/article/details/86130696, docker run --it --v/dataset:/dataset --v/inference:/inference --v/result:/result floydhub/pytorch:0.4.0-py2.29/inference/inference.sh. File "/blobtoolkit/blobtools2/lib/fasta.py", line 77, in parse It looks like the tutorials may have been updated in the last few weeks, so I will take a look there for now. This should give you access to the viewer from outside the Docker container so now instead of using docker exec to run blobtools view, you should be able to open a web browser on your local machine and visit http://localhost:8080/view/dataset/membranacea_dataset/cumulative to see the cumulative plot. File "./blobtools2/blobtools", line 48, in Loading sequences from /blobtoolkit/data/membranacea.contigs.fasta action-link: you have created a network with the name my-project-2. (and then nothing happens), When I attempt the cumulative plot: File "./blobtools2/blobtools", line 48, in waiting for element cumulative_save_png, (& the same thing happens for snail_save_png). I made some changes to the directory structure in the container and it looks like I forgot to update the path in the example command, the taxdump is available in the container at /blobtoolkit/databases/ncbi_taxdump so the command should contain. Hey Jon, I did not. docker run -d --rm --name btk -p 8080:8080 -p 8000:8000 -v /Users/amcdonnell/Analyses/blobtools/datasets:/blobtoolkit/datasets -e VIEWER=true genomehubs/blobtoolkit:latest, output to screen I tried running it a few different times with different paths, and the most successful try so far gave me a ModuleNotFoundError: No module named 'docopt': (base) mac-amcdonnell-p:~ amcdonnell$ docker run -it --rm --name btk -u $UID:$groups -v /Users/amcdonnell/Analyses/blobtools/datasets:/blobtoolkit/datasets -v /Users/amcdonnell/Analyses/blobtools/membranacea.contigs.fasta:/blobtoolkit/data genomehubs/blobtoolkit:latest ./blobtools2/blobtools create --fasta /blobtoolkit/data/membranacea.contigs.fasta --taxid 1234 --taxdump taxdump /blobtoolkit/datasets/membranacea_dataset Well occasionally send you account related emails. I am still getting the same error as my last post. Loading http://localhost:8002/view/dataset/membranacea_dataset/snail?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg (base) mac-amcdonnell-p:blobtools amcdonnell$ docker exec -it btk ./blobtools2/blobtools view --host http://localhost:8080 --out output --view cumulative membranacea_dataset meta=meta) I ran it with genomehubs/blobtoolkit:latest and got the error again. docker run -it -v D:\Program Files\RASA\myproject-2\rasa-x-waapi\myenv\Docker:/app -p 5005:5005 --net my-project-2 rasa/rasa:2.8.2 shell, Try folder names lowecase i.e. 0it [00:00, ?it/s] It looks like it ran; it parsed all my contigs, but then I got this error: . Docopt is installed and when I test the container it runs fine but on some systems it seems that there can be an issue with finding the package. It's irritating! Fetching datasets/membranacea_dataset.snail.png Loading http://localhost:8080/view/dataset/membranacea_dataset/cumulative?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg Hey, thanks, Richard! For an alternative that should get around this, you are on the right track with running. I've updated the container image with the latest blob tools code and set an explicit PYTHONPATH so hopefully this will start working for you if you docker pull genomehubs/blobtoolkit:latest to get the most recent version. See 'docker run --help'. Will take slightly longer but won't hit the error above: Your create command doesn't include any BLAST hits so the cumulative plot won't work. Could you try adding -e PYTHONPATH=/home/blobtoolkit/miniconda3/envs/btk_env/lib/python3.6/site-packages to your docker command and see if that helps? The response should look like. Can you post the full command you are running? 'range': [min(gc_portions), max(gc_portions)] docker: invalid reference format. . I'm trying to run blobtoolkit in a docker container locally by modifying your suggested code. . Hey again. Is it a problem with my -v paths? error is likely caused by a space in one of the - v flags so hopefully won't happen again with the suggested command above. The docker: invalid reference format. I think I have some blast output somewhere, I will find it and try the cumulative plot again. http://localhost:8080/view/dataset/membranacea_dataset/cumulative?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg, http://localhost:8080/view/dataset/membranacea_dataset/cumulative, http://localhost:8002/view/dataset/membranacea_dataset/snail?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg, processing tig00030305=37045=1suggestBubble=noCircular=no: : 2122it [01:02, 33.81it/s]. `(base) mac-amcdonnell-p:blobtools amcdonnell$ docker exec -it btk \, Initializing viewer || 15/15 seconds A waste of life! The paths/result and/inference and/dataset You can configure shared paths from Docker -> Preferences -> File Sharing. The text was updated successfully, but these errors were encountered: Your command should probably look more like: the -v options bind directories on your local system to directories in the btk container. Is this something that needs to be corrected in the blobtoolkit docker image/container? Tried using the quickstart code, but getting the error: Cant understand what Im doing wrong. I've rebuilt the container with updated dependencies so the latest container version is 1.3.1, if you still can't see anything with: Could you send me the results of ls -al /Users/amcdonnell/Analyses/blobtools/datasets and attach the output of docker logs btk and docker exec -it btk curl 'http://localhost:8080' so I can try to work out what is going wrong. I got the taxdump error again: . from docopt import docopt 0it [00:00, ?it/s]cat: /blobtoolkit/data/membranacea.contigs.fasta: No such file or directory I updated the container and restarted analyses. By clicking Sign up for GitHub, you agree to our terms of service and So, when I try generate the snail plot using either method, I end up with the message "waiting for element snail_save_png". I'm sorry if I keep making silly errors. Ok thanks. docker: Error response from daemon: Mounts denied: Please explain me this above run command. Ah, looks like I'd missed out on adding the taxdump when rebuilding the Docker image with all the other dependencies inside. As BlobToolKit runs inside the container, it can't see the external file paths so any files you refer to in the blobtools create command have to be relative to the container filesystem.