Our local instance of galaxy is working fine (galaxy_dist version).
I tried enabling PAGES by including enable_pages = True in the universe_wsgi.ini file first in the beta section which gave me problems. Searching the wiki and user forum indicates the enable statement should be in the [app::main] section, so I did. No luck either and same error as below.
I do get a SAVED PAGES option (instead of PAGES option as described in the wiki) under USER menu where I can create pages and see them listed. But when I select edit contents I only get an empty box at the top left of the page editor and a script error (below attached) on ie8.
Do I miss some prerequisite for PAGES to work correctly? Or is this an ie8 generic problem since I just checked in firefox and it seems to work. IE8 is unfortunate our embedded/default company web browser.
Any help appreciated.
---------Script error of the page ---------------
Gebruikersagent: Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 6.1; WOW64; Trident/4.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; InfoPath.3)
Tijdstempel: Mon, 27 Sep 2010 08:00:35 UTC
Message: Id, string or number expected
Message: Id, string or number expected
Recently I followed the guide on
So I created two ini files, one for the web apps and 1 for the runner. Now
is my question, what purpose does the universe_wsgi.ini serve. As I found
out yesterday is that this ini is still used by the manage_db.sh script.. I
never updated this universe_wgsi.ini file, although I moved to another
database. So this script updated the wrong database.. error on my side I
guess, but should I really keep 3 universe_wsgi files? And if so, what
should be in which, as I now have most of the parameters in all three ini
I've been trying to run R in Galaxy.
1. Running it as "R" is a hassle, because Galaxy cannot deal with
source and input file and output file using "--args" and "<" (< in xml) and ">" (> in xml).
2. Running it through "perl" is also a hassle, because Galaxy needs to have
an input file through the cmd line, whilst "R" needs:
- input file (the location of it, not the content)
- source file (.R file)
- output file
BUT you need to pipe -this- input for perl through to R VIA the system() call.
Anybody any luck with this?
(everything runs without Galaxy btw, but that is not the aim)
This solves it I think.
I re-directed this to galaxy-user, because it is clear that some of you do not know this either.
From: James Taylor [james(a)jamestaylor.org]
Sent: 21 September 2010 13:21
To: Bree, Freddy de
Subject: Re: [galaxy-user] running R in Galaxy
On Sep 21, 2010, at 7:16 AM, Bree, Freddy de wrote:
> Thanks for the tip, but do you mean in Galaxy?
> From: James Taylor [james(a)jamestaylor.org]
> Sent: 21 September 2010 13:06
> To: Bree, Freddy de
> Cc: galaxy-user(a)lists.bx.psu.edu
> Subject: Re: [galaxy-user] running R in Galaxy
> On Sep 21, 2010, at 5:30 AM, Bree, Freddy de wrote:
>> 1. Running it as "R" is a hassle, because Galaxy cannot deal with
>> source and input file and output file using "--args" and
>> "<" (< in xml) and ">" (> in xml).
> We use a small shell script called r_wrapper.sh which is included in
> the distribution.
I found a bug in extracting FATSA sequence tool in galaxy.
I extracted sequence of this location chr10 123229360 123229525 fgfr2 0
And I checked back in UCSC browser by pasting the same location. The
sequences are completely different (hg18).
Could you please help me in this issue
> Yes, you can generate a FASTQ file with dummy quality scores from a
> FASTA file. Use the Combine FASTA and QUAL into FASTQ tool under
> NGS: QC and manipulation-->ROCHE-454 DATA. For the Quality Score
> File, leave it set with the default option ("Selection is
> Optional"). The quality value will be ~ for each base
> On Sep 17, 2010, at 4:10 PM, Ada Sedova wrote:
>> Dear galaxy,
>> I have some sequence data that is in fasta format, and I would
>> really like to run bowtie on it for mapping. The bowtie article
>> claims that bowtie can map with fasta files, but galaxy does not
>> allow it. Is there anything I can do to fix this? For instance, is
>> there a way to add some kind of q values to the file so it will run?
>> galaxy-user mailing list
I have some sequence data that is in fasta format, and I would really like
to run bowtie on it for mapping. The bowtie article claims that bowtie can
map with fasta files, but galaxy does not allow it. Is there anything I can
do to fix this? For instance, is there a way to add some kind of q values to
the file so it will run?
I'm getting errors in running our solid to fastq conversion tool. I'm not
sure why, we have sqlite installed... This is the error. Perhaps i'm
overlooking another dependency?
Traceback (most recent call last):
line 7, in ?
ImportError: No module named sqlite3
Thanks in advance.