Moderator: James Taylor

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James Taylor470
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Posts by James Taylor

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Why does Galaxy use a 'history' and not a 'directory' to manage user content?
... While Galaxy stores metadata about a dataset (name, datatype, tags) in its database, the data are actually stored in files on disk. This is what makes it possible to integrate existing command line tools that alrady work on files. The history is one view of a set of files in Galaxy that corresponds ...
written 15 months ago by James Taylor470
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Answer: A: Optional workflow input parameters
... Such a workflow cannot be created in Galaxy currently. Support for conditionally choosing different subpaths in a workflow is planned. Progress will be update here (https://github.com/galaxyproject/galaxy/issues/1928) under Workflow > Decision Points. ...
written 15 months ago by James Taylor470
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Comment: C: I have some problems to deal with macs.
... Hello jsleecsbl! We believe that this post does not fit the main topic of this site. Not Galaxy related. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we ...
written 15 months ago by James Taylor470
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Answer: A: how to restart the local galaxy server without cancel the running jobs
... I believe when using the local job runner running jobs will be cancelled. Jobs that have not yet run (e.g. queued or gray) will still be started after the server restarts as long as track_jobs_in_database is set as Martin said. For running jobs to survive a restart you need to use a separate DRM ...
written 15 months ago by James Taylor470
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Comment: C: Quality Report
... On Wed, Nov 6, 2013 at 12:54 PM, Benjamin Osei-agyeman < Is the quality poor across the entire read, or just at one end? You can improve overall quality in two ways. By filtering out lower quality reads (the Filter by Quality tool or Filter FASTQ tool) or by trimming a portion of the reads (the ...
written 4.1 years ago by James Taylor470
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Answer: A: Secure File Upload Gateway For Galaxy
... Galaxy's FTP support uses ProFTPD, which has modules for both TLS (FTPS) and SFTP. -- James Taylor, Associate Professor, Biology/CS, Emory University On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras ...
written 4.2 years ago by James Taylor470
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Answer: A: Need Your Helps About Galaxy
... As I said before, there is no easy way to do this. You just need to dump the old database and load into the new database. I would suggest making a copy of the old database with a current version of Galaxy. The migration scripts will then bring it up to date so you will have identical schemas. You sh ...
written 4.2 years ago by James Taylor470
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Answer: A: Tophat Problem On A New Local Instance
... Regarding (2), have you installed bowtie and tophat on your Mac Pro? Galaxy does not currently automatically install all of the software needed to run tools (we are working on this through the toolshed, but at the moment it is a manual process). Dependencies of various tools included in the distrib ...
written 4.5 years ago by James Taylor470
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Answer: A: How Do I Add Ray To Galaxy Central In The Tool Shed ?
... And I really want you to do this! No, we are gradually moving all the tools out of galaxy-central into the Tool Shed. You probably want to look at this page: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-p arty_tool_dependency_installation_and_compilation_with_installed_re ...
written 4.5 years ago by James Taylor470
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Comment: C: How To Share An History With A Specific User ?
... Sarah, when you share with a specfic user, it will not show up under the "Shared Data" section since that is only for published items. The person you share it with should see it under "Histories Shared with me" which is in the History options menu: -- James Taylor, Assistant Professor, Biology/CS, ...
written 4.5 years ago by James Taylor470

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Scholar 15 months ago, created an answer that has been accepted. For A: Optional workflow input parameters

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