Thank you for your replay. I am new to Galaxy, and nobody else in my research
group is working on it. I access Galaxy via the web page http://galaxy.nbic.nl,
without a local instance. Does this mean that I am using a cloud Galaxy? Or am
I using the public galaxy server?
However, when I read the instructions in one of the links you kindly sent me,
the web page for the main server is called https://usegalaxy.org. When I try to
log in on that web page, it comes back with the message that this user does not
exist. Now I am very confused about the very basic thing as via which instance
I access Galaxy. Could you please clarify this for me? I am sorry for asking
such a basic question.
Thank you in advance for your help.
Ilse van de Vondervoort
On 06 Jan 2014, at 19:46 , Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hello Lise,
> This is in your own local instance? If so, the instance will need to have a
> few configuration changes and reference genomes added (and the server you are
> using must have the proper resources available to run the tools - the general
> rule is if you can run the tool line command, then it will almost certainly
> run in Galaxy - see the source binary for required resource information). If
> you are using a cloud Galaxy, the genomes can just be added. Resources on a
> cloud instance can be scaled up if you find that you need more (memory, more
> nodes, etc) to achieve the throughput you want, or to run large datasets.
> For a local instance, the basic install instructions are here:
> Then, you need to proceed to the Advanced Production configuration (#3) to
> Once you are ready to add genomes (local or cloud), make sure your tool
> dependencies are set up (Bowtie2, etc). The builds.txt file needs to list the
> genomes you are working with, then the genomes and indexes need to be added.
> We provide our genomes via rsync if you want to use them, or you can download
> a genome from any source you want and create indexes yourself. If you use our
> reference genomes, then it will be easier to use your data on the public
> server, if that is a future goal (using the same reference genome throughout
> an analysis is very important). Bowtie2 indexes are not yet available for all
> genomes, but these not difficult to create. Instructions for this are in
> these two wikis:
> Hopefully this helps. If anything has been misunderstood, please let us know
> and provide more details. Please keep all replies on the mailing list so that
> the development community can help with troubleshooting.
> Galaxy team
> On 1/6/14 8:46 AM, Ilse van de Vondervoort wrote:
>> Dear developers,
>> I encountered a problem when I wanted to map rat microRNA sequencing data
>> (FASTQ file, after FASTQ Groomer) to the reference genome (see attached
>> screenshot). I am unable to select any build-in reference genome, and I
>> haven’t used any myself thus I can’t select one from my history.
>> Hopefully, this is an easy to overcome issue.
>> Kind regards,
>> <Mail Attachment.png>
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> Jennifer Hillman-Jackson
Please keep all replies on the list by using "reply all"
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