User: Robert Curtis Hendrickson

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Posts by Robert Curtis Hendrickson

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Comment: C: Posting Supplementary Information On Galaxy Server
... Jennifer, We are also interested in using PSU galaxy to host a history for out supplemental methods. Based on your response, it looks like PSU is willing to support that use case. However, I'd like to know how long we can count on that link being available. Searching the wiki for "publish" or "sup ...
written 4.1 years ago by Robert Curtis Hendrickson130
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Text Manipulation > Compute > C1[1:C1.Find("(")] Fails
... Folks, I have a column c1 that has entries like "GXP_297346(PVALB/human)". I'm trying to use Text Manipulation > Compute to strip off the "(...)" portion, leaving only the accession (which can vary in length). I have tried a variety of things that work in my python command line, but fail here, ...
gmod written 6.4 years ago by Robert Curtis Hendrickson130 • updated 6.3 years ago by Russell Bell30
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Comment: C: How To Re-Use A Parameter In A Workflow?
... Daniel, Great. That exactly and perfectly solves my problem! Thanks so much. Regards, Curtis To: Robert Curtis Hendrickson Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to re-use a parameter in a workflow? Hi Curtis, In the workflow editor, you can specify a parameter name wi ...
written 6.4 years ago by Robert Curtis Hendrickson130
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How To Re-Use A Parameter In A Workflow?
... Galaxy Users, I have a workflow where I'd like the user to input a value once, say a number of nucleotides. That value would then be used as an input parameter to several different tasks, for example, to two instances of "Operate on Genomic Intervals > Get flanks" , where it would be used both f ...
galaxy written 6.4 years ago by Robert Curtis Hendrickson130 • updated 6.4 years ago by Daniel Blankenberg ♦♦ 1.7k
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Comment: C: Error Running Cufflinks On Galaxy
... Jen, We are running into the same problem on our local install of galaxy. We're running Cufflinks v.1.0.1, on a BAM file (accepted_reads) from TopHat run on mm9 based RNAseq data (paired-end 25mer), and pulled down the changes made to galaxy last month to support the 1.0.1 version of Cufflinks. We ...
written 6.5 years ago by Robert Curtis Hendrickson130
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Ftp And Command Line Access In Galaxy
... Nate, The Galaxy's ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? If not, would it be eas ...
galaxy written 6.5 years ago by Robert Curtis Hendrickson130 • updated 6.5 years ago by Peter Cock1.4k
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Comment: C: Can I Merge Histories?
... Jen, Thanks for all your quick responses. I have found Googling documentation for Galaxy extremely hard, because it is such a common term. How I wish it had been misspelled (intentionally)! I work in an informatics core, where several of us collaborate on projects. We have a local Galaxy installat ...
written 6.5 years ago by Robert Curtis Hendrickson130
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Comment: C: Can I Merge Histories?
... Jen Thanks, that works, mostly. All the task numbers are now changed, but not updated in the names of tasks. Additionally, I don't see any way to identify the input tasks aside from the names that were generated. Again, I've lost by trace back ability. If I look in the "info" the "names" of the in ...
written 6.5 years ago by Robert Curtis Hendrickson130
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Can I Merge Histories?
... Folks, Is there some way I can merge histories? I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and contras ...
galaxy written 6.5 years ago by Robert Curtis Hendrickson130 • updated 6.5 years ago by Dannon Baker3.6k
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Answer: A: Re: Ucsc->Emboss/Fuzznuc->Ucsc Workflow?
... Jen, Thanks for all your help. Here's the final Galaxy workflow for doing FUZZNUC on a BED file from UCSC Table Browser, then producing BED file that you can view in UCSC. http://main.g2.bx.psu.edu/u/curtish-uab/w/fuzznucucscbed I do not include the "Get Flank" operation in this base workflow, bu ...
written 6.5 years ago by Robert Curtis Hendrickson130

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