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:j...@bx.psu.edu]
Sent: 06 December 2013 16:00
To: Arno, Matthew; galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] Galaxy tool error report from matthew.a...@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-...@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:j...@bx.psu.edu]
> Sent: 28 November 2013 23:59
> To: galaxy-b...@bx.psu.edu; Arno, Matthew
> Subject: Re: [galaxy-bugs] Galaxy tool error report from 
> matthew.a...@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-b...@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.a...@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


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