User

Stephen Fleming

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Total activity 125
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Recent activity by Stephen Fleming

  • Support folders (in addition to files) in the Terra data table

    Currently, when I click on an entry in the Terra data table that points to a folder (by which I mean a google bucket path that is not a concrete file), I see something like this Technically the me...

    • 3 followers
    • 3 comments
    • 7 votes

  • Alternative to archiving workflow metadata

    I've now been running WDLs in Terra long enough that some older workflow details have been archived.  In my experience, it is very common to need to go back past a year to look for details of old w...

    • 2 followers
    • 1 comment
    • 1 vote

  • The "where did this file come from?" feature

    Can Terra implement a "where did this file come from?" feature?The idea would be that you can point to a file in the Terra data table, and (if it was generated by a workflow) it will tell you which...

    • 3 followers
    • 3 comments
    • 9 votes
    • Completed

  • Scatter: over chunks rather than for each

    Hello! I have a specific question about scattering in a WDL.  What I want to do is a lot like this scatter (file in file_array) { call task{input: file=file}} except that, in my case, it is horrib...

    • 2 followers
    • 4 comments
    • 0 votes

  • Cromwell execution directory

    Cromwell question: is there an environment variable that I can access from within a running task's command block that specifies the Cromwell execution directory (google bucket) ?

    • 2 followers
    • 4 comments
    • 1 vote

  • Possible to clone a notebook VM?

    Hello! I want to enable somebody else on my billing project to work in the exact same notebook environment I am working in. I realize that the real goal is to have a nice docker image so that you c...

    • 2 followers
    • 4 comments
    • 0 votes

  • Failed to check notebook status: "Autosave Failed!"

    Hello! I do a lot of work in Terra notebooks these days.  Fantastic feature, thanks for creating it!   One thing that is a huge bummer is that if I'm working on a notebook, I sometimes get a messag...

    • 6 followers
    • 34 comments
    • 1 vote

  • Notebooks: folder structure for organization

    It would really help us out if we could organize our Terra notebooks using a file folder structure within our workspace. Once we get a lot of notebooks saved (and we use them for development too, n...

    • 1 follower
    • 1 comment
    • 4 votes

  • Jupyter Lab

    Jupyter notebooks have been a great addition in Terra.  How about considering Jupyter Lab? https://jupyterlab.readthedocs.io/en/stable/ That way, instead of having a sort of separate interface for ...

    • 5 followers
    • 3 comments
    • 4 votes

  • Terra workflow descriptions: display in markdown

    In the Firecloud UI, in the Methods Repo, the description of a method seems to be formatted using markdown.  Links show up as actual links you can click on.  Code syntax is highlighted as a `parame...

    • 1 follower
    • 1 comment
    • 1 vote