User: Guy Reeves

gravatar for Guy Reeves
Guy Reeves710
Reputation:
710
Status:
Trusted
Location:
Germany
Last seen:
25 minutes ago
Joined:
2 years, 2 months ago
Email:
r*****@evolbio.mpg.de

Posts by Guy Reeves

<prev • 181 results • page 1 of 19 • next >
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Comment: C: What Galaxy tools can preprocess VCF file before running the SNPEff annotation p
... Snpeff should accept any properly formed vcf. There should be no need to preprocess it. Is data type = vcf? What is the problem you are having? ...
written 3 days ago by Guy Reeves710
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Proxy Error on importing files by FTP
... Hi While uploading files using getdata>upload file> chose FTP file on our own galaxy instance, we keep getting the following error when we do this for long lists of files. The same file that gives an error and goes red will be fine if we do it again. the error we get is **Proxy Error The ...
ftp proxy import error written 4 days ago by Guy Reeves710
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Comment: C: How to split a merge piared data using ncbi SRA tools?
... 1Are you on usegalaxy.org? 2are you using the tool 'getdata>EBI SRA' 3 what happens to the downloaded dataset ( grey , yellow , green, red?). does it have an extension in its name? Galaxy should automatically deal with .gz files without you noticing. I will try to help once I have answers to t ...
written 19 days ago by Guy Reeves710
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Answer: A: How to successfully export large numbers of files outside of galaxy- as history
... You will need to install from the toolshed ‘Bundle Collection Download a collection of files (Galaxy Version 1.0.1)’- unfortunately this is not currently available on usegalaxy.org. I have successfully tested this procedure for BAM files (you get a data and an index file) and fastq and fasta files. ...
written 20 days ago by Guy Reeves710
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Answer: A: How to split a merge piared data using ncbi SRA tools?
... Hi Personally, I avoid having to split SRA data by using the EBI site which mirrors the same SRA data as NCBI but also given the option of already split files (the ID numbers are the same on both). Also by using the 'getdata>EBI SRA' tool which It think is on all galaxy instances you also hav ...
written 23 days ago by Guy Reeves710
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Comment: C: I can download individual galaxy files but not exported-histories
... HI Jen I think it would be a great feature to have, but I have no idea how much work it would require to do. I will look into using tools from the toolshed that compress a list if datasets. I assume the compressed file could be then be successfully downloaded using wget or curl. I am looking int ...
written 23 days ago by Guy Reeves710
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How to successfully export large numbers of datasets outside of galaxy- as history 'export to file' will not work
... Using the 'Download tip: Big data' from https://wiki.galaxyproject.org/Support I can get very large files out of Galaxy without having to download them to the machine I am running the web browser on. This works well for single files e.g. curl -o bam_Fam1_n13_fam2_n18 'http://172.16.0.140/galaxy/dat ...
export history wget curl download written 25 days ago by Guy Reeves710
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Comment: C: An entertaining read about BWA, Picard, GATK
... Trying to use GATK on Galaxy is not a path to happiness, the conditions placed on GATK use do not fit will the open source approach of galaxy and so it has not been well ssupportedfor a longtime . ...
written 26 days ago by Guy Reeves710
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Answer: A: An entertaining read about BWA, Picard, GATK
... Hi Alex We have two galaxy instances one conventional and one with docker. When I have had problems with installing tools on our main conventional one I mostly find that the galaxy docker instance has no problem. We would use only docker but we have issues with updating a number of libraries which ...
written 26 days ago by Guy Reeves710
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Comment: C: Extract command line from Galaxy run?
... Isn't this info available to non-admin user through the same veiw details button? ...
written 26 days ago by Guy Reeves710

Latest awards to Guy Reeves

Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How to successfully export large numbers of files outside of galaxy- as history
Scholar 20 days ago, created an answer that has been accepted. For A: increasing the number of concurent jobs that can be run
Scholar 6 months ago, created an answer that has been accepted. For A: increasing the number of concurent jobs that can be run
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Scholar 16 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 16 months ago, created an answer that has been accepted. For A: Attaching annotations to Sequences
Centurion 17 months ago, created 100 posts.
Scholar 20 months ago, created an answer that has been accepted. For A: Attaching annotations to Sequences
Student 23 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 23 months ago, created 50 posts within first three months of joining.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: variable inputs workflow
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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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