Feature Request: Add Support for GenBank Format Download to Facilitate Non-Professional Users #4063
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hi there, I know @scottcain has been trying out this branch for users on wormbase It has been in the works for a long time, but I think that it is getting closer to ready! |
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For a few WormBase releases, I've held back the save track data functionality from the production version (since the functionality hasn't been part of an official JBrowse 2 release) but with WS290, released about a month ago, the JBrowse version that is running on WormBase proper (as opposed to just the staging site) has the save track data option. See for example: https://wormbase.org/tools/genome/jbrowse2/?session=share-fNO7Q3m5rP&password=VU5n1 and click on the vertical ... on the track label and select "save track data" from the context menu. |
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Hello @cmdcolin and @scottcain , Thank you for your prompt responses. I am greatly appreciative of the progress with the "Save track data" feature in JBrowse 2. Through your efforts, our laboratory has successfully adopted the GenBank download functionality on WormBase, which has proven to be incredibly useful and a significant aid in our work. However, we also handle datasets that are not featured on WormBase. This presents a unique challenge, as we need to provide access to these datasets for non-professional users, who are our primary focus in certain projects. In trying to implement the advancements from PR #3439, I have encountered several technical difficulties. Despite my best efforts, I keep running into errors that are beyond my technical expertise to resolve. I would greatly appreciate a more user-friendly option, such as a Conda package or a Docker image, which would make it more accessible for users like myself. Could you advise on the availability of such options, or suggest other convenient installation methods that could cater to users with less technical background? Thank you for your consideration and looking forward to the further development of this feature. |
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Hi @lybCNU , Unfortunately, at the moment, I don't have the bandwidth to create a generic use JBrowse 2 docker image, but such a thing would be nice to have. Can I ask what are the nature of the problems you are running into: are they related to configuring/running a web server, installing JBrowse 2 with the jbrowse-cli, or configuring JBrowse 2 (creating a config.json), or something else entirely? |
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Hi, @scottcain I'm not sure if I understand the installation process correctly. As per my understanding, I downloaded the When try to install nodejs18 on our lab server, I got this. Loaded plugins: langpacks, product-id, search-disabled-repos, subscription-manager This system is not registered with an entitlement server. You can use subscription-manager to register. nodesource-release-nodistro-1.noarch.rpm | 10 kB 00:00:00 I don't want to modify the glibc of our lab server. Instead I installed nodejs and yarn with conda. But I don't known how to install yarn install v1.22.21 warning package-lock.json found. Your project contains lock files generated by tools other than Yarn. It is advised not to mix package managers in order to avoid resolution inconsistencies caused by unsynchronized lock files. To clear this warning, remove package-lock.json. Then, I tried install to install yarn install v1.22.19 [1/4] Resolving packages... I can install the jbrowse2 with conda. Is that possible to add the |
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@lybCNU I can see the route you've taken, I think you made some good steps but there are alternate ways of doing this I'm just going to summarize the steps you took, and then say why they may not lead to the right outcome, and then provide a potential alternative path
All of that to say, you can use our pre-built version of jbrowse web for this branch without going through all those steps! You can run jbrowse create --branch save_track_data output_dirand it will download the latest version of jbrowse-web, from that beta branch save_track_data Then, you can put output_dir in your web server directory e.g. /var/www/html/ and access it like http://localhost/output_dir This way, all you need to do is install the jbrowse CLI tool (npm install -g @jbrowse/cli). Hopefully that works using the conda nodejs environment you have. If not, we can try to go from there! We don't have any default docker or conda tooling for jbrowse 2, but the pre-built instructions don't require too advanced of a dev environment so I hope that helps! |
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Hi, @cmdcolin I am writing to express my sincere gratitude for your guidance and support. Following your latest advice, I am thrilled to report that I have successfully implemented the functionality we needed in JBrowse 2. Thank you very much for your exceptional support. |
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@lybCNU thanks for the kind words. I just wanted to add, the genbank format is quite tricky, so i just tried my best to make it work. even downloaded a trial of snapgene, but my trial ran out at this point! if you spot anything wrong with it, or anything that can be improved, let us know |
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Hi @cmdcolin Furthermore, I would like to recommend the Thank you again! |
Hello JBrowse2 development team,
I have encountered an issue with JBrowse2: it currently seems to be unable to support downloading files in GenBank format. In particular, I am in need of the join feature in GenBank files, which is crucial for describing gene structures that span multiple non-contiguous regions.
I would like JBrowse2 to add support for downloading files in GenBank format, making it more accessible for users without a programming background. This support should include the ability to handle join statements, accurately reflecting complex gene structures.
The current alternative involves downloading the sequence and then manually adding features using SnapGene or other software. However, this process becomes particularly cumbersome when dealing with gene structures that span multiple non-contiguous regions. Not only is it time-consuming, but it also requires a level of expertise with these software tools that many users, especially those without a programming background, may not possess.
The addition of this feature would greatly enhance the appeal of JBrowse2 within the bioinformatics community, especially for non-professional users seeking straightforward solutions.
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