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GMOD / docker-apollo

:whale: Apollo 2.X Docker Image
GNU General Public License v3.0
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Tracks view give "Object Response" Error #41

Closed csmibrahim closed 5 years ago

csmibrahim commented 5 years ago

Hi, I have a working docker image from the GitHub but I get object Response error when I add tracks as shown below.

Screenshot 2019-05-28 at 20 22 52

The error in itself is not helpful to track the problems.

Other GitHub issue shows similar error and was fixed by adding permission in the httpd file. https://github.com/GMOD/jbrowse/issues/1242 But I am not sure where can I add this in Docker.

csmibrahim commented 5 years ago

Any idea? Regards

cmdcolin commented 5 years ago

Looks like a 404 file not found for this URL. The JBrowse side of things did a couple updates to improve this error message, apologies for the vagueness. I don't know if there is something specific about docker apollo that causes this though

nathandunn commented 5 years ago

@csmibrahim Some questions:

csmibrahim commented 5 years ago

Are you able to add a GFF3 file? -- No Many Perl packages missing and errors How are you mounting / running? -- I followed the step on the GitHub page. Running production using the build created by quay.io. Where are the mounted files located? -- All files at jbrowse-data folder as in the Example. How are you adding the BAM files (manually or via upload)? Manually. Do you see any tomcat error logs (you have to be in the system to see them)? Not sure where I can see them.

nathandunn commented 5 years ago

@csmibrahim I am traveling this week, but I will try to test when I can. I will need a bit more detail:

Are you able to add a GFF3 file? -- No Many Perl packages missing and errors

Can you add a track by clicking on "New Track" here?

image

How are you mounting / running? -- I followed the step on the GitHub page. Running production using the build created by quay.io.

A specific command would be really helpful here, as I have lots of commands. Feel free to obscure any local paths if need to, of course.

Where are the mounted files located? -- All files at jbrowse-data folder as in the Example.

Could you provide a specific link to the example. Sorry, we just have a ton of doc.

How are you adding the BAM files (manually or via upload)? Manually.

Can you post your trackList.json then. Thanks.

Do you see any tomcat error logs (you have to be in the system to see them)? Not sure where I can see them.

Let's not worry about that yet, but thanks for looking.

csmibrahim commented 5 years ago

I followed the steps as in https://github.com/GMOD/docker-apollo read.me

Running with: docker run -it -v /jbrowse/root/directory/:/data -v postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest

Here the tracklist: { "tracks" : [ { "key" : "Reference sequence", "storeClass" : "JBrowse/Store/Sequence/StaticChunked", "category" : "Reference sequence", "label" : "DNA", "seqType" : "dna", "type" : "SequenceTrack", "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", "chunkSize" : 20000 }, { "label" : "CDB_bam", "key" : "CDB BAM", "urlTemplate" : "CDB.bam", "storeClass" : "JBrowse/Store/SeqFeature/BAM", "type" : "JBrowse/View/Track/Alignments2" }, { "type" : "JBrowse/View/Track/Alignments2", "storeClass" : "JBrowse/Store/SeqFeature/BAM", "urlTemplate" : "PDB_sub.bam", "key" : "PDB BAM", "label" : "PDB_bam" } ], "formatVersion" : 1 }

nathandunn commented 5 years ago

So to clarify you have something like:

nathandunn commented 5 years ago

It might work to upload the organism and GFF3 file:

image

csmibrahim commented 5 years ago

Yes, I have all of that and I uploaded the organism already from the interface successfully and all are fine. Until I added tracks and try to see them on Jbrowser the error come. For GFF3, when I run the flatfile-to-json i got endless missing Perl packages but this is not the issue her now.

nathandunn commented 5 years ago

Can you use the new track feature?

https://github.com/GMOD/docker-apollo/issues/41#issuecomment-497090491

Also, I updated the quay image if you want to pull it docker pull quay.io/gmod/docker-apollo:latest

csmibrahim commented 5 years ago

Yes, this work perfectly.

Previously I was following the data loading steps as in https://genomearchitect.readthedocs.io/en/latest/Data_loading.html.

Is there any new documents other than this I can follow?

nathandunn commented 5 years ago

@csmibrahim There is not. I will plan it for the 2.4.0 release.

However, if you want to add any here to detail your process, https://github.com/GMOD/Apollo/blob/develop/docs/Data_loading.md that would be awesome.

I can reformat / reorganize it later.

nathandunn commented 5 years ago

Can we close this, or are you still having trouble with BAM files using this mechanism?