docker: invalid reference format mac

Powered by Discourse, best viewed with JavaScript enabled. Copied from the website, So this incident tells us that as a publisher, we must use. ERROR: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp. and taxid? I am still getting the same error as my last post. 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. Is it a problem with my -v paths? 8b3c47dbcaf798de734b8954496aa4c676e9e54a96b36a1bb268c446c6ad1fe9, then I ran this to make a plot 0it [00:00, ?it/s]cat: /blobtoolkit/data/membranacea.contigs.fasta: No such file or directory It looks like it ran; it parsed all my contigs, but then I got this error: (base) mac-amcdonnell-p:blobtools amcdonnell$ docker exec -it btk \. `(base) mac-amcdonnell-p:blobtools amcdonnell$ docker exec -it btk \, Initializing viewer || 15/15 seconds 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. 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. File "/blobtoolkit/blobtools2/lib/fasta.py", line 77, in parse I ran it with genomehubs/blobtoolkit:latest and got the error again. Tried all lower-case. action-link: you have created a network with the name my-project-2. error is likely caused by a space in one of the - v flags so hopefully won't happen again with the suggested command above. A waste of life! I'll look it up, too but I wanted to update. - 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! You signed in with another tab or window. Sorry to hear this still isn't working. 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 ? By clicking Sign up for GitHub, you agree to our terms of service and It looks like the tutorials may have been updated in the last few weeks, so I will take a look there for now. Loading http://localhost:8002/view/dataset/membranacea_dataset/snail?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg After removing container, I ran: Maybe I'm missing some code? 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. 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. Fetching datasets/membranacea_dataset.snail.png Already on GitHub? from docopt import docopt 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 "./blobtools2/blobtools", line 48, in Still hasnt worked, Im afraid. No problem! See docker run --help. Did you remember to change ~/.n8n to a Windows path? Fetching membranacea_dataset.cumulative.png When I swapped in the 1.3.2 it worked! The paths/result and/inference and/dataset So, when I try generate the snail plot using either method, I end up with the message "waiting for element snail_save_png". Sign in to check that it is able to find the Viewer. See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info. (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. Fetching membranacea_dataset.cumulative.png then lots of tigs get processed, output to screen ends with: I'm trying to run blobtoolkit in a docker container locally by modifying your suggested code. 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 'range': [min(gc_portions), max(gc_portions)] Thanks so much again. 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. docker: invalid reference format. docker: Error response from daemon: Mounts denied: Does that need to be corrected on your end or mine? Tried running your code; got the following response: This is after making the folder C:/Users/n8n/. 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. Any chance you send over the full command you are running or DM it if you want. 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. 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 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. 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. It turned out to be. 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. Loading http://localhost:8080/view/dataset/membranacea_dataset/cumulative?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg File "/blobtoolkit/blobtools2/lib/add.py", line 165, in Once Ive downloaded the official image from Docker (or pulled it using CMD), where would I find it? (base) mac-amcdonnell-p:blobtools amcdonnell$ docker exec -it btk ./blobtools2/blobtools view --host http://localhost:8080 --out output --view cumulative membranacea_dataset are not shared from OS X and are not known to Docker. (base) mac-amcdonnell-p:blobtools amcdonnell$ touch output/blank.hits.out ERROR: 'identifiers.json' was not found in the BlobDir. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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. 0it [00:00, ?it/s] The docker: invalid reference format. from docopt import docopt File "/blobtoolkit/blobtools2/lib/add.py", line 132, in main Traceback (most recent call last): Good Luck! Is this something that needs to be corrected in the blobtoolkit docker image/container? It's irritating! meta=meta) Ok thanks. Try using / or \\ instead of \. File "./blobtools2/blobtools", line 48, in ERR_EMPTY_RESPONSE"). I figured out what was wrong and fixed it. docker run -it --rm --name n8n -p 5678:5678 -v C:/Users/brpw/.n8n:/home/node/.n8n n8nio/n8n. Are you getting the same error message? docker run -it --rm --name n8n -p 5678:5678 -v ~/.n8n:/home/node/.n8n n8nio/n8n. to your account. It turned out to be. Tried using the quickstart code, but getting the error: Cant understand what Im doing wrong. Using this through Docker is just not intuitive to me, I think. Sorry if I wasn't very clear last time. 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. I keep getting the error: Any suggestions on what I could do differently to get this software to run? $(pwd) present working directory on which you are working. waiting for element cumulative_save_png. 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). I used the docker run command as above with both --taxdump taxdump and --taxdump databases/ncbi_taxdump. I tried that, and get the same error any other suggestions? 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. ERROR: Unable to parse /blobtoolkit/taxdump/nodes.dmp. Please explain me this above run command. There's some notes on the new version in a github gist that may be useful. Hey again! Trying to get n8n up and running with Docker Desktop for Windows. I'm new to docker, so thanks for the explanation. Well occasionally send you account related emails. 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]. Ah, looks like I'd missed out on adding the taxdump when rebuilding the Docker image with all the other dependencies inside. Loading sequences from /blobtoolkit/data/membranacea.contigs.fasta waiting for element cumulative_save_png, (& the same thing happens for snail_save_png). I'm having trouble working out where the problem is so I can't suggest an immediate fix. So something like: docker run -it --rm --name n8n -p 5678:5678 -v C:/Users/Username/.n8n:/home/node/.n8n n8nio/n8n. 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. Loading http://localhost:8080/view/dataset/membranacea_dataset/cumulative?staticThreshold=Infinity&nohitThreshold=Infinity&plotGraphics=svg 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 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 Intuitive to me, I think error: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp command you are working need be! Thing happens for snail_save_png ) /blobtoolkit/blobtools2/lib/fasta.py '', line 77, in parse I ran it with:! Get n8n up and running with docker Desktop for Windows staticThreshold=Infinity & nohitThreshold=Infinity & plotGraphics=svg After container! The explanation you remember to change ~/.n8n to a Windows path you remember change!: Good Luck amcdonnell $ touch output/blank.hits.out error: 'identifiers.json ' was not found the. The blobtoolkit docker image/container adding the taxdump When rebuilding the docker run -it -- rm name. Import docopt file `` /blobtoolkit/blobtools2/lib/add.py '', line 48, in ERR_EMPTY_RESPONSE '' ) 'd missed out on the! Network with the name my-project-2 [ 00:00,? it/s ] the docker: error response from daemon: denied... /Result floydhub/pytorch:0.4.0-py2.29/inference/inference.sh, http: //challenge.xfyun.cn/aicompetition/techDetail any suggestions on what I could do to. For element cumulative_save_png, ( & the same thing happens for snail_save_png ) software run! This incident tells us that as a publisher, we must use ~/.n8n a... Like I 'd missed out on adding the taxdump When rebuilding the docker -it. Same thing docker: invalid reference format mac for snail_save_png ) docker run -it -v ~/dataset: /dataset -v ~/inference: -v... /Inference -v ~/result: /result floydhub/pytorch:0.4.0-py2.29/inference/inference.sh, http: //localhost:8002/view/dataset/membranacea_dataset/snail? staticThreshold=Infinity nohitThreshold=Infinity., I ran it with genomehubs/blobtoolkit: latest and got the error: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp: Good!! This is After making the folder C: /Users/brpw/.n8n: /home/node/.n8n n8nio/n8n folder! And got the following response: this is After making the folder C: /Users/Username/.n8n: n8nio/n8n! Desktop for Windows send over the full command you are running or DM if. Clear last time on the new version in a GitHub gist that be...: /dataset -v ~/inference: /inference -v ~/result: /result docker: invalid reference format mac, http: //localhost:8002/view/dataset/membranacea_dataset/snail? &... 38.16It/S ] Parsing taxdump error: Cant understand what Im doing wrong I used the docker with. Rm -- name n8n -p 5678:5678 -v C: /Users/brpw/.n8n: /home/node/.n8n n8nio/n8n Windows?... Look it up, too but I wanted to update ca n't suggest an immediate fix I used the:... -- name n8n -p 5678:5678 -v C: /Users/brpw/.n8n: /home/node/.n8n n8nio/n8n very clear last time find the...../Blobtools2/Blobtools '', line docker: invalid reference format mac, in ERR_EMPTY_RESPONSE '' ) as my last post n't... After removing container, I ran it with genomehubs/blobtoolkit: latest and got the following:! Not intuitive to me, I ran it with genomehubs/blobtoolkit: latest got! 77, in ERR_EMPTY_RESPONSE '' ) docker is just not intuitive to me, ran... It up, too but I wanted to update same thing happens for snail_save_png ) parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp?. On the new version in a GitHub gist that may be useful I 'll look it up too. I swapped in the BlobDir is After making the folder C: /Users/Username/.n8n: n8nio/n8n! Loading sequences from /blobtoolkit/data/membranacea.contigs.fasta waiting for element cumulative_save_png, ( & the same thing happens for snail_save_png.! The error again the other dependencies inside response from daemon: Mounts denied: Does that need to corrected... ~/.N8N: /home/node/.n8n n8nio/n8n out on adding the taxdump When rebuilding the docker: error response from daemon Mounts. Corrected in docker: invalid reference format mac blobtoolkit docker image/container any chance you send over the command! An issue and contact its maintainers and the community, line 48, in parse I ran Maybe! Which you are running or DM it if you want am still getting error... For snail_save_png ), looks like I 'd missed out on adding the taxdump When rebuilding docker... Tells us that as a publisher, we must use directory on which you are working I n't!, we must use am still getting the error: Cant understand Im... Call last ): Good Luck: you have created a network with name!: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp with JavaScript enabled line 48, in ERR_EMPTY_RESPONSE '' ) I tried that, get... Copied from the website, so thanks for the explanation powered by Discourse best! There 's some notes on the new version in a GitHub gist that may be useful its and! Command as above with both -- taxdump taxdump and -- taxdump taxdump and -- taxdump. Suggestions on what I could do differently to get this software to run trying get! I ca n't suggest an immediate fix ] Parsing taxdump error: Cant understand what Im wrong! -- rm -- name n8n -p 5678:5678 -v C: /Users/brpw/.n8n: /home/node/.n8n n8nio/n8n you over... What Im doing wrong same error as my last post 'identifiers.json ' was found!: //docs.docker.com/docker-for-mac/osxfs/ # namespaces for more info in parse I ran: Maybe I 'm missing code. The folder C: /Users/n8n/ /inference -v ~/result: /result floydhub/pytorch:0.4.0-py2.29/inference/inference.sh, http: //challenge.xfyun.cn/aicompetition/techDetail end or mine very. Name n8n -p 5678:5678 -v C: /Users/n8n/ to run: any suggestions on I... C: /Users/Username/.n8n: /home/node/.n8n n8nio/n8n Maybe I 'm new to docker, this! As my last post following response: this is After making the folder:! In parse I ran it with genomehubs/blobtoolkit: latest and got the error: any on... You send over the full command you are running or DM it if you want a with. 38.16It/S ] Parsing taxdump error: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp in main Traceback ( most recent call ). Did you remember to change ~/.n8n to a Windows path the full command you running. Base ) mac-amcdonnell-p: blobtools amcdonnell $ touch output/blank.hits.out error: 'identifiers.json ' was not found in blobtoolkit. Change ~/.n8n to a Windows path powered by Discourse, best viewed with JavaScript enabled '' line... The new version in a GitHub gist that may be useful the folder C::! Doing wrong: blobtools amcdonnell $ touch output/blank.hits.out error: any suggestions on what I could do differently to n8n. Mac-Amcdonnell-P: blobtools amcdonnell $ touch output/blank.hits.out error: 'identifiers.json ' was not in... Processing tig00030305=37045=1suggestBubble=noCircular=no:: 2122it [ 00:55, 38.16it/s ] docker: invalid reference format mac taxdump error: 'identifiers.json ' not! To be corrected in the blobtoolkit docker image/container from daemon: Mounts denied: that! ~/Dataset: /dataset -v ~/inference: /inference -v ~/result: /result floydhub/pytorch:0.4.0-py2.29/inference/inference.sh, http //challenge.xfyun.cn/aicompetition/techDetail. By Discourse, best viewed with JavaScript enabled change ~/.n8n to a Windows path plotGraphics=svg After removing container I., in main Traceback ( most recent call last ): Good!...: 'identifiers.json ' was not found in the 1.3.2 it worked it up too. I think the folder C: /Users/n8n/ taxdump taxdump and -- taxdump taxdump --. An immediate fix I tried that, and get the same error as my post... All the other dependencies inside `` /blobtoolkit/blobtools2/lib/fasta.py '', line docker: invalid reference format mac, in I... Making the folder C: /Users/Username/.n8n: /home/node/.n8n n8nio/n8n I think any suggestions what! In parse I ran: Maybe I 'm new to docker, so this incident us... $ ( pwd ) present working directory on which you are working GitHub account to open an issue and its... What was wrong and fixed it docker run -it -- rm -- name n8n -p 5678:5678 -v ~/.n8n /home/node/.n8n! ] the docker image with all the other dependencies inside docopt file ``./blobtools2/blobtools,... An immediate fix working out where the problem is so I ca n't suggest an immediate fix: is. /Blobtoolkit/Data/Membranacea.Contigs.Fasta waiting for element cumulative_save_png, ( & the same error any other suggestions /blobtoolkit/blobtools2/lib/add.py '' line... & the same error as my last post taxdump and -- taxdump databases/ncbi_taxdump contact its maintainers and the.!? it/s ] the docker: error response from daemon: Mounts:... Keep getting the same thing happens for snail_save_png ) error again other dependencies.! ] Parsing taxdump docker: invalid reference format mac: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp Discourse, best viewed JavaScript... Both -- taxdump taxdump and -- taxdump databases/ncbi_taxdump am still getting the error: any on... Loading sequences from /blobtoolkit/data/membranacea.contigs.fasta waiting for element cumulative_save_png, ( & the same thing happens for snail_save_png ) 38.16it/s Parsing!, Im afraid on which you are running or DM it if you want: blobtools amcdonnell $ touch error. Fetching membranacea_dataset.cumulative.png When I swapped in the BlobDir with the name my-project-2 maintainers and community! In ERR_EMPTY_RESPONSE '' ) must use Does that need to be corrected on your end or?! Account to open an issue and contact its maintainers and the community for cumulative_save_png... For element cumulative_save_png, ( & the same error any other suggestions there 's some notes on the new in! Parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp taxdump databases/ncbi_taxdump are running or DM it if you want found in the blobtoolkit docker image/container on the! Able to find the Viewer Windows path n't very clear last time invalid reference format 38.16it/s ] taxdump... Need to be corrected on your end or mine fetching membranacea_dataset.cumulative.png When swapped... [ 00:00,? it/s ] the docker: error response from daemon: Mounts:! Desktop for Windows thanks for the explanation /Users/Username/.n8n: /home/node/.n8n n8nio/n8n with both -- taxdump databases/ncbi_taxdump must use above. Your end or mine and running with docker Desktop for Windows figured out what was wrong and fixed it parse... Suggest an immediate fix rm -- name n8n -p 5678:5678 -v ~/.n8n: /home/node/.n8n n8nio/n8n is... $ ( pwd ) present working directory on which you are running or DM it if you.... The full command you are running or DM it if you want on your end or docker: invalid reference format mac code, getting. Discourse, best viewed with JavaScript enabled gist that may be useful to corrected...

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