We are interested in collecting more information about the user, e.g.
which lab they're part of etc, as they register to use our local mirror of
galaxy. Is there an easy way to add these fields to the registration
page; is it also easy to store these values to the (galaxy) database?
I would like to use MySQL instead of sqlite to store my data. I coudn't
find on the Galaxy web site a HOWTO or some guidelines to do it. I only
found some lines that might need to be changed/enabled in the
#database_file = database/universe.sqlite
database_connection = mysql:///galaxy
#database_engine_option_echo = true
#database_engine_option_echo_pool = true
#database_engine_option_pool_size = 10
#database_engine_option_max_overflow = 20
Could you point out to some doc or briefly describe what I need to do in
order to go for mysql?
Are there any plans to support other DBMS's (like Oracle for instance)?
I recently came to know about NGS analysis on galaxy during ISMB.
Getting excited I tried couple of things basically to play with it.
Few comments : I may have interepretted something described below in a
wrong way. My apologies before hand.
On a standalone installation of galaxy while I was trying to explore
one FASTQ(sequence) file. It takes considerable (> 20 min) for a fastq
file to get uploaded (2 GB). I am not sure what is the rationale
behind that. Ideally I think there should be no need to upload such
heavy files into the workspace. They could actually be used straight
away by the path specified. Also is there any way to access the
scripts for analysis on the command line. I know this undermines the
main aim of working with galaxy but rite now I am concerned about the
I will be happy to discuss more about this in case you have some
comments/questions for me.
Bioinformatics Software Engineer
Institute for Genome Sciences
School of Medicine, Univ of Maryland
801, W. Baltimore Street, Baltimore, MD 21209
We (BioBike) would like to do to Galaxy what Galaxy does to the UCSC browser, that is, be able to UI+programmatically (i.e., without download/upload of tables) get data from Galaxy to BioBike so that a BioBike user can then carry out next-level-up symbolic analysis on the data that has been molded, folded, and joined by Galaxy. Can someone point me to a description of the API that would enable us to do this?
I wrote a tool that splits a FASTA file into n output files, each one of
a predefined maximum size. The program could return the number of files
or a list of filenames...
Is it possible to define the number of outputs dynamically (nr of output
files dependent on input-filesize)?
till now i experimented with:
<tool id="seqan_splitter_1" name="FASTA splitter">
<description>Splits input files into pieces of desired size</description>
<param name="source" type="data" format="fasta" label="input fasta file"/>
<param name="size" type="integer" label="Size in Megabyte of
each output file" value="500" optional="false"/>
<param name="files" type="hidden" value="10"/>
#for $i < $files
<data format="fasta" name="\$i" label="Splitted file"/>
<data format="text" name="log_report" label="Detailed log report
I am a new galaxy user. I am trying to upload coding exons of specific region from ucsc genome browser but I end up with loading coding exons of all splice variants/isoforms. As a result some exons are repeated many times (depending upon how many isoforms the crossponding gene has) which I don't want. Can somebody help me how can I have a list of coding exons in which each exon is represented only once irrespective of how many splice variants/isoforms the gene has? Thanks a lot
Atteeq Ur Rehman
National Institute on Deafness and Other Communication Disorders,
National Institutes of Health,
Room 2A-19, 5 Research court, Rockville, MD, USA, 20850.
Lab Ph. No. 301-402-9059
I have a little how to do question and was hoping somebody knows the
I have a metagenomic data set with reads of lengths between 100 and
1000 bp. Now I want to create a dataset from my original dataset, with
sequences of exact 200bp. I know I can use the filter tool to extract
all reads longer than 199bp from the original data set. But then I
want to cut off all the sequence bit that is longer than 200bp. so I
end up with only a dataset of exactly 200bp. Does anybody know how I
can do that in Galaxy. I was thinking of some of the EMBOSS tools, but
they only see the first sequence and not all the other sequences in my
Any ideas are welcome.
Dr. Thomas H.A. Haverkamp
Centre for Ecological and Evolutionary Synthesis (CEES)
Dept. of Biology
University of Oslo
P.O. Box 1066 Blindern
0316 Oslo Norway
Phone: +47 22 85 44 00
Mobile: +47 48 09 49 32
Hi galaxy users!
We would like to integrate a new datasource in our galaxy system. We
want data to be inserted into galaxy via copying them directly from
fileservers instead of uploading them through a http connection- maybe
via some browser-based "explorer" who gives access to certain folders-
Is there any galaxy-build in feature which may support something like this?