Re: [galaxy-dev] Best practices for utilising Unique Molecular Indexing (UMI's)

Hi Tony, please see inline answers > On 27. Mar 2018, at 16:45, Brooks, Tony wrote: > > Hi Charles > Thanks for replying. Yes, I'd definitely be interested in the command line > version. we’ll try to push the version we have in conda tomorrow. > I'm assuming I can use je retag to add the

[galaxy-dev] Remove entry from Tool Data Table using via Data Manager

Hello, I'm working on galaxy integration for an MLST tool called MentaLiST: https://github.com/WGS-TB/MentaLiST/tree/master/galaxy I've created data managers that create kmer databases and store their locations in a Tool Data Table. I'd like to allow users to remove entries from the Tool Data Ta

Re: [galaxy-dev] Tool to download galaxy datasets locally

Hi Evan, you can have a look at https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/ Hope that helps! Cheers, Nicola On 27/03/18 16:03, evan clark wrote: Has anyone attempted to write a tool that a

Re: [galaxy-dev] Shiny in Galaxy

Dear Mohamed, Karim, Hans, I don't know if you are still looking for a Galaxy Interactive Environment with Shiny. But in collaboration with Yvan's team, we have also developed a generic Shiny GIE for the Workflow4Metabolomics project. You can find it with an example on GitHub at the following

[galaxy-dev] Tool to download galaxy datasets locally

Has anyone attempted to write a tool that allows copying of galaxy datasets locally, i.e. without downloading via http. We have scenario where there are some additional tools available only via command line and it would be very useful to be able to directly copy galaxy datasets from the dataset

Re: [galaxy-dev] Best practices for utilising Unique Molecular Indexing (UMI's)

Hi Charles Thanks for replying. Yes, I'd definitely be interested in the command line version. I'm assuming I can use je retag to add the UMI from a separate read to my sample fastq (already demultiplexed by bcl2fastq) then use the de-markdupes already in Galaxy to dedupe? Would this work? Bt