Hi - Question from a biologist on thin ice here... I've setup a galaxy instance on cloudman AWS, and I'd like to upload some data using FTP. When I used the public galaxy server previously I used 'usegalaxy.org' as the host in FileZilla FTP program; what do I use for the host in the cloud instance? It just says 'localhost' on the galaxy upload page...which doesn't work? I presume the instance has some specific/temporary host/server ID, somewhere...where would I find it? Cheers, Matt ---------------------- Matthew Arno, Ph.D. Genomics Centre Manager Franklin-Wilkins Building (Waterloo Campus) King's College London T +44 (0) 207 848 4286 www.kcl.ac.uk/genomics The contents of this email are strictly confidential. It may not be transmitted in part or in whole to any other individual or groups of individuals. This email is intended solely for the use of the individual(s) to whom they are addressed and should not be released to any third party without the consent of the sender. -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: 06 December 2013 16:00 To: Arno, Matthew; galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from matthew.arno@kcl.ac.uk Hi Matt, Using a cloud galaxy is intended to be as simple as possible, and once it is going, really is in most ways the same exact experience as using the public Main server, except that your jobs will run quicker (if you allocate resources to them) and you will have much more space. This is the only way to get more processing power. Please see: http://usegalaxy.org/cloud And for support/help, the galaxy-dev@bx.psu.edu mailing list is good. We can help where you have trouble. Many biologist and small labs go this route. http://wiki.galaxyproject.org/MailingLists Another option is a SlipStream appliance. All options are here: http://wiki.galaxyproject.org/BigPicture/Choices Please review and let us know if you need more help, Jen Galaxy team On 12/6/13 7:31 AM, Arno, Matthew wrote:

Dear Jennifer - thanks for the email support - I will give it a try.

Also, I was wondering whether it's possible to buy a little more access to Galaxy? I don't have any kind of cluster/server set up I can use or set up galaxy on. I have no idea how to use a cloud 'instance' - I am just a biologist who is just about able to use your browser GUI, and just about able to understand things.

So basically I need to know how much would it cost for a bit more storage and a bit more processing power? Something in between the public server and your other suggestions.

Thanks, Matt

---------------------- Matthew Arno, Ph.D. Genomics Centre Manager Franklin-Wilkins Building (Waterloo Campus) King's College London T +44 (0) 207 848 4286 www.kcl.ac.uk/genomics

The contents of this email are strictly confidential. It may not be transmitted in part or in whole to any other individual or groups of individuals. This email is intended solely for the use of the individual(s) to whom they are addressed and should not be released to any third party without the consent of the sender.

-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: 28 November 2013 23:59 To: galaxy-bugs@bx.psu.edu; Arno, Matthew Subject: Re: [galaxy-bugs] Galaxy tool error report from matthew.arno@kcl.ac.uk

Hello Matt,

You are following an RNA-seq example? Here is one from our team in case you haven't seen it: https://usegalaxy.org/u/jeremy/p/interactive-rna-seq-with-trackster http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-se q

But let's get it prepped correctly first -

It looks like the upload was incomplete or the file is truncated locally (before upload, perhaps as you were moving it around on your own system). If you use the tool "Text Manipulation -> Select last lines from a dataset" at default on dataset #4, then look at the output, you will be viewing the end of the file.

I ran FastQC on just the first few sequences, and your data has quality score encoding as "Sanger / Illumina 1.9". This translates to the datatype ".fastqsanger" in Galaxy. You can just assign this, then run FastQC to proceed with trimming, etc.

Full details are here: http://wiki.galaxyproject.org/Support#Dataset_special_cases

It looks as if browser upload was used? For files near/over 2G, FTP is required: http://wiki.galaxyproject.org/Support#Loading_data

Best!

Jen Galaxy team

On 11/28/13 6:54 AM, galaxy-bugs@bx.psu.edu wrote:

...

GALAXY TOOL ERROR REPORT ------------------------

This error report was sent from the Galaxy instance hosted on the server "usegalaxy.org" --------------------------------------------------------------------- - ------- This is in reference to dataset id 7146374 from history id 1694389 --------------------------------------------------------------------- - ------- You should be able to view the history containing the related history item

18: FASTQ Groomer on data 4

by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.

usegalaxy.org/history/view?id=af8aac32a6b50fb7 --------------------------------------------------------------------- - ------- The user 'matthew.arno@kcl.ac.uk' provided the following information:

hi - I am trying to read in some FastQ files from an Ion Proton run: is there a specific workflow/pipeline for this? They are RNAseq/transcriptomic samples, so I want to be able to run the tophat workflow. I have tried the FastQ groomer which has failed like this and even fastQC report fails, so I am guessing it has something to do with the format from ion proton...

Cheers, matt --------------------------------------------------------------------- - ------- job id: 6151484 tool id: fastq_groomer job pid or drm id: 189480 --------------------------------------------------------------------- - ------- job command line: None --------------------------------------------------------------------- - ------- job stderr: Traceback (most recent call last): File "/galaxy/main/server/tools/fastq/fastq_groomer.py", line 42, in <module> if __name__ == "__main__": main() File "/galaxy/main/server/tools/fastq/fastq_groomer.py", line 22, in main for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type, apply_galaxy_conventions = True ) ): File "/galaxy/main/server/lib/galaxy_utils/sequence/fastq.py", line 466, in __iter__ yield self.next() File "/galaxy/main/server/lib/galaxy_utils/sequence/fastq.py", line 504, in next raise e Exception: Invalid FASTQ file: could not find quality score of sequence identifier @UIPGM:01360:12780.

--------------------------------------------------------------------- - ------- job stdout: There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.

The reported error is: 'Invalid FASTQ file: could not find quality score of sequence identifier @UIPGM:01360:12780.'. The last valid FASTQ read had an identifier of '@UIPGM:01349:12777'. The error in your file occurs between lines '39516093' and '39516095', which corresponds to byte-offsets '2257518563' and '2257518593', and contains the text (30 of 30 bytes shown):

@UIPGM:01360:12780 ATCTGATACG

--------------------------------------------------------------------- - ------- job info: None --------------------------------------------------------------------- - ------- job traceback: None --------------------------------------------------------------------- - ------- (This is an automated message). -- Jennifer Hillman-Jackson http://galaxyproject.org

-- Jennifer Hillman-Jackson http://galaxyproject.org