Dear Jennifer, 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. Kind regards, Ilse van de Vondervoort On 06 Jan 2014, at 19:46 , Jennifer Jackson <jen@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: https://wiki.galaxyproject.org/Admin/GetGalaxy Then, you need to proceed to the Advanced Production configuration (#3) to here: https://wiki.galaxyproject.org/Admin/GetGalaxy#Advanced_Configuration

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: https://wiki.galaxyproject.org/Admin/Data%20Integration https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

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.

Best,

Jen 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, Ilse

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