User: James Taylor

gravatar for James Taylor
James Taylor320
Reputation:
320
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Location:
United States
Last seen:
4 years, 1 month ago
Joined:
12 years, 6 months ago
Email:
j****@bx.psu.edu

Posts by James Taylor

<prev • 32 results • page 1 of 4 • next >
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Answer: A: Upload Genome Index To Galaxy For Bowtie Alignment?
... Jeffrey, is this a publicly available genome build (e.g. In genbank?). It may be easier to provide the index. -- jt (composed on my phone) On Jun 8, 2010, at 12:19 PM, "Whyte, Jeffrey" ...
written 8.1 years ago by James Taylor320
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Comment: C: User Reference Vs. Built-In Index
... The indexing should be automatic. We'll need to look at it in more detail. -- jt (composed on my phone) ...
written 8.2 years ago by James Taylor320
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Comment: C: Database Schema
... Hi Nils, Currently most structure parallelism in Galaxy is at the between tool level, individual tool runs still usually run on a single node. There are certain tools that manage their own parallelism. We're currently working on better support for within job parallelism, and in particular extendin ...
written 8.2 years ago by James Taylor320
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Re: Strand Info In The Second Query Is Not Recognized By "Interval Intersection"
... The behavior of this tool is intentional. Regardless of which direction a feature is encoded in, we consider to features having any overlapping DNA to intersect. However, it would be good for this tool to have an option to handle your use case (only consider intervals overlapping if on the same str ...
written 8.2 years ago by James Taylor320 • updated 8.2 years ago by Daniel Blankenberg ♦♦ 1.7k
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Answer: A: Universe_Wsgi.Ini -- "True" Case Sensitivity?
... It should be. If you find a case where it isn't, it is a bug. Thanks! ...
written 8.2 years ago by James Taylor320
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Comment: C: Unsubscribe
... If you wish to unsubscribe, please visit the list management link: http://lists.bx.psu.edu/listinfo/galaxy-user Sorry to see you go. -- jt ...
written 8.3 years ago by James Taylor320
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Comment: C: Pysam Egg
... I think we're working around this, but you need to make sure you are building from our modified pysam: http://bitbucket.org/kanwei/kanwei-pysam I can't see any good reason why this should have a dependency on glib, but in any case we try to build all eggs with static linking, so we'll fix this. ...
written 8.5 years ago by James Taylor320
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Answer: A: Dataset Visivility Policy
... Hello, By default on the main Galaxy datasets are public. If you set the permissions by adding roles required to access the dataset this should no longer be the case. I have verified this on Galaxy main: ...
written 8.6 years ago by James Taylor320
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Answer: A: Command Line Execution
... Hi Jordan, There are currently two possibilities. First, one can simulate a web client from a command line script. Galaxy is fairly restful, so this is not too hard in practice, although you probably need to login and do cookie management. Second, all of the programs Galaxy runs are command line pr ...
written 8.6 years ago by James Taylor320
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Answer: A: Request For Showing Output Plots In Galaxy Frame
... Matthew, What browser are you seeing this behavior on? Clicking the "eye" icon should display PDF datasets in the middle pane, and I just verified that it does on main using Safari. However, how PDFs are displayed is dependent on browser and plugin issues. -- jt ...
written 8.7 years ago by James Taylor320

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