User: Guy Reeves

gravatar for Guy Reeves
Guy Reeves630
Reputation:
630
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Trusted
Location:
Germany
Last seen:
3 days, 17 hours ago
Joined:
2 years, 1 month ago
Email:
r*****@evolbio.mpg.de

Posts by Guy Reeves

<prev • 167 results • page 1 of 17 • next >
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Error is this a problem with the tool wrapper or with the tool installation?
... HI I just installed Beagle4.0 from the main tool shed on my galaxy instance. I know I had it working on other instances but currently it goes red. The last line of the error is IOError: [Errno 2] No such file or directory: '/home/galaxy/galaxy/database/job_working_directory/012/12957/tmpfz8obq/b ...
wrapper beagle error written 19 days ago by Guy Reeves630
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Answer: A: Filtering Variants using Snpsift filter and SnpEff
... HI (countRef() < 1)= keep site if the the total number of samples with 0/0 is less that 1 ie zero. (countHet() <1)= keep site if the the total number of samples with 0/1 is less that 1 ie zero. (AND ) is used ensure that only sites where there are no 0/0 AND no 0/1 ie sites with only 1/1 ...
written 29 days ago by Guy Reeves630
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Answer: C: Filtering Variants using Snpsift filter and SnpEff
... I find it hard to follow what you are trying to do. Do you want to output a file with only those sites were all samples are 1/1? If this is what you want to do this try ((countRef() < 1) AND (countHet() <1)) To be honest I have not tested it (and I can see that any sites with missing data woul ...
written 4 weeks ago by Guy Reeves630
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Comment: C: Workflow cannot run
... that is strange. are you logging in as a registered user ? If you are I do not really have any more ideas can you share the workflows and dataset on use galaxy? If you do I will try wth my account. Cheers Guy ...
written 7 weeks ago by Guy Reeves630
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Comment: C: Workflow cannot run
... Is the box checked "Send results to a new history " just above the ' Run workflow' button you use to start the workflow? Are you using usegalaxy.org? ...
written 7 weeks ago by Guy Reeves630
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Comment: C: Workflow cannot run
... Is the box checked "Send results to a new history " just above the ' Run workflow' button you use to start the workflow? If it is then you do not expect to see any datasets (jobs) to be created in the history you started in. You will need to look at the 'view al histories' view and look at the n ...
written 7 weeks ago by Guy Reeves630
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Comment: C: No queued jobs showed in the history after I ran a workflow
... Is the box checked "Send results to a new history " just above the ' Run workflow' button you use to start the workflow? If it is then you do not expect to see any datasets (jobs) to be created in the history you started in. You will need to look at the 'view al histories' view and look at the n ...
written 7 weeks ago by Guy Reeves630
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Comment: C: SNP Check for homozygous and heterozygous
... you may be able to use 'VCFfilter' tool which is on usegalaxy.org but I am not convinced ...
written 9 weeks ago by Guy Reeves630
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Comment: C: getting number of SNPs, insertion/deletion from VCF with VCFfilter
... as "locally cached" does not give you the hg19 option you want I guess you are not working on usegalaxy.org. I suggest you register for an account and move your data there (or at least part of it). Then you can see what works and then work on installing reference genomes onto your local galaxy ins ...
written 9 weeks ago by Guy Reeves630
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Answer: A: SnpSift difficulty with Filter expression in Galaxy, which is fine on the comman
... This whole issue was due to an old version being installed on usegalaxy.org which did not the documentation which was current and for the latest version. When i installed from the toolshed a more updated version on my galaxy instance I had no problems. ...
written 9 weeks ago by Guy Reeves630

Latest awards to Guy Reeves

Scholar 5 months ago, created an answer that has been accepted. For A: increasing the number of concurent jobs that can be run
Voter 15 months ago, voted more than 100 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Without 'Available inputs are:' it is not possible to rename datasets in workflo
Scholar 15 months ago, created an answer that has been accepted. For A: Attaching annotations to Sequences
Centurion 16 months ago, created 100 posts.
Scholar 19 months ago, created an answer that has been accepted. For A: Attaching annotations to Sequences
Student 22 months ago, asked a question with at least 3 up-votes. For What is the ROD file -Need help with "Realigner Target Creator" tool
Rising Star 22 months ago, created 50 posts within first three months of joining.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: variable inputs workflow
Supporter 22 months ago, voted at least 25 times.
Student 2.1 years ago, asked a question with at least 3 up-votes. For What is the ROD file -Need help with "Realigner Target Creator" tool

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