Hello all,
I am a new Galaxy admin/developer, so if this is as stupid question please
be kind.
I am trying to add the ability for a user to choose additional parameters
for Tophat for Illumina. After analyzing the Python and XML files
in /galaxy-dist/tools/ngs_rna, I came to the conclusion that
, though it's definitely possible to configure an upstream proxy to do
so. Are you using a setup similar to
https://wiki.galaxyproject.org/Admin/Config/nginxProxy#SSL ?
-Dannon
On Wed Feb 18 2015 at 4:34:51 PM Scott Szakonyi scott.b.szakony...@nd.edu
wrote:
Hello all,
Just curious
Hello all,
I have a user who is getting the following error when analyzing a FASTQ
file using TopHat for Illumina.
TopHat v2.0.10
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core]
Hello all,
In testing our servers for security vulnerabilities, we've detected some
cross site scripting and SQL injection problem on our Galaxy server. Is
that something that should be reported as a bug/problem? I did search the
Trello board but didn't find any open security related items.
, 2015 at 10:16 AM, Scott Szakonyi
scott.b.szakony...@nd.edu wrote:
Hello all,
In testing our servers for security vulnerabilities, we've detected some
cross site scripting and SQL injection problem on our Galaxy server. Is
that something that should be reported as a bug/problem? I did search
:/bin/sh: -c: line 14: syntax error:
unexpected end of file
If you have any suggestions about this error, I'd be pleased to attempt to
resolve it.
Best,
Scott
On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi <scott.b.szakony...@nd.edu>
wrote:
> Hi Martin,
>
> Thanks very much
; wrote:
>
>> Hi Scott, Martin,
>>
>> there was still a small problem in cairo.
>> I made a PR to fix this (
>> https://github.com/galaxyproject/tools-devteam/pull/300)
>> I should have paid a bit more attention ...
>>
>> Cheers,
>> Marius
>>
>>
installed tools",
> then click on "Advanced Search" on top, then click on "Deactivated or
> uninstalled" and click on "Activate or reinstall" on Trimmomatic menu.
>
> Cheers,
> Nicola
>
>
> On 20/11/15 18:07, Scott Szakonyi wrote:
&
ure Galaxy plans to use a smart caching proxy to handle
> all source codes required by the Tool Shed installations. This effort is
> lead by Eric Rasche and you can see it here
> https://github.com/galaxyproject/cargo-port
>
> Thank you for the report (and for using Galaxy :)).
&g
ov 20, 2015 at 9:33 AM, Nicola Soranzo <nsora...@tiscali.it> wrote:
> Hi Scott,
> the mercurial mirror is not up to date unfortunately, see this previous
> discussion:
>
>
> http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html
>
> Ch
Hi all,
If I try to build a new track browser from a custom build, I'm not able to
see any of the datasets in my build after clicking add datasets and
selecting my workflow from history. Am I doing something wrong, or is there
a problem? I've been able to recreate this on both my local server and
Hello all,
I'm having issues installing Trimmomatic and Picard tools from the
toolshed. The errors are of the following form (Trimmomatic used for the
example).
Trimmomatic 0.32 package shows an installation error.
Error details:
File
Hi all,
Of course, we need to upload large data files. I understand that the common
way to achieve this is with an FTP server, but due to our situation setting
one up is problematic. Does Galaxy have any mechanism for retrieving data
from cloud resources such as Dropbox, Box, or Google Drive?
Hello all,
I have some biologists here at Notre Dame who use the Picard
Tools CreateSequenceDictionary application as part of their workflow. I've
tried to locate it in the toolshed but all the Picard Tools versions that
are available don't seem to include it. Does anyone know where I might find
amFile.
>
> If you think this is not the best approach, please open an issue at
> https://github.com/galaxyproject/tools-devteam
>
> Chees,
> Nicola
>
>
> On 01/02/16 14:02, Scott Szakonyi wrote:
>
> Hello all,
>
> I have some biologists here at Notre Dame
requirement on the wiki?
> https://wiki.galaxyproject.org/Admin/GetGalaxy
>
> Peter
>
> On Fri, Feb 26, 2016 at 5:49 PM, Scott Szakonyi
> <scott.b.szakony...@nd.edu> wrote:
> > Hi,
> >
> > I'm having trouble uploading BAM files in our development environment.
> Other
&g
Hello all,
I'm having an issue with a missing dependency for readline 6.2. When I try
to install or repair, I get the following error message:
configure: error: in
`/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2':
configure: error: cannot compute suffix of
Sorry, I was a bit premature. I did find the INSTALLATION.log file, but it
only contains the original error message. I can't seem to find a config.log
file anywhere.
Thanks!
Scott
On Fri, Mar 11, 2016 at 8:19 AM, Scott Szakonyi <scott.b.szakony...@nd.edu>
wrote:
> Hello Peter,
>
&
ill
> give you some clues as to what the problem could be.
>
> HTH
>
> Best wishes
>
> Peter
>
> On 09/03/16 20:33, Scott Szakonyi wrote:
>
>> Hello all,
>>
>> I'm having an issue with a missing dependency for readline 6.2. When I
>> try to ins
Hello,
I'm trying to set our Galaxy instance to put Dataset and Temporary files on
a Symlinked drive, as there isn't sufficient room on the Galaxy server to
handle those files. However, I can't get it to work. Even though I've
changed these settings, Galaxy still seems to be creating large
Hi all,
I'm having some difficulties with logging into my production website. I get
the following error message in the logs:
galaxy.web.framework.webapp WARNING 2016-04-06 18:47:41,852 User logged in
as 'userID' externally, but has a cookie as 'use...@vectorbase.org'
invalidating session
This
Hello,
I'm having an odd problem after updating to the latest version of Galaxy.
My users prepare data for analysis using data manager tools, such as
"data_manager_bwa_mem_index_builder". When an attempt is made to run one of
these tools, a pop up window opens stating "Tool request failed" and
Hi all,
I know this is not a technical question per se, but this seems my best
option for getting better information.
I am planning on attending the Galaxy Conference this year. I administrate
the Galaxy server for VectorBase (vectorbase.org), but I'm a computer
scientist, not a bioinformatics
Hi all,
Sorry to be repetitive, but this issue is really blocking our efforts to
develop the workflow that we need in our instance of Galaxy. If anyone has
any familiarity with the issue described below, please let me know. I
really need to get this solved.
One of my co-administrators is having
gt; help you decide what to attend.
> From my experience in addition to scientists there are many admins and
> developers attending the conference so you should be able to find your
> flock easily.
>
> Plus we are all nice. :)
>
> Best,
> Martin
>
> On Fri, Mar 4, 201
Hi all,
I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It
appears the script is unable to import sqlalchemy, but my understanding is
that Galaxy can't function without it, so I'm at a loss to explain. Here's
the error I'm getting:
$ sh
Hello,
I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04.
However, when I attempt to do so, I get an error, and git log shows I'm
still on 16.01.
$ sudo git checkout master && pull --ff-only origin master
M tool-data/all_fasta.loc.sample
Already on 'master'
-bash: pull:
-Dannon
>
> On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi <scott.b.szakony...@nd.edu>
> wrote:
>
>> Hi all,
>>
>> I'm getting an error when executing the cleanup scripts in Galaxy 16.01.
>> It appears the script is unable to import sqlalchemy, but my
d and you get back a bunch of JSON about the
> tool. I tried looking in the Galaxy code to see if I could quickly
> determine where the /root controller is, but I wasn't successful. Perhaps
> this is now enough information that one of the developers might be able to
> help us.
>
<h...@fmi.ch> wrote:
> Hi Scott
>
> Can you explain a little bit more what you mean by "file references that
> are no longer valid in one of his histories"?
>
> What happens when your user tries to delete the affected history item?
>
>
> Regards, Hans-Rud
Hello all,
We have indexed a genome using the appropriate data manager, for GATK, and
our reference is showing up and working for individual walkers in GATK
2.8. When designing a workflow, however, the reference genome is not
appearing as an option for many walkers, including indel realigner and
’m not positive, but this behavior may be related to this issue:
>
> https://github.com/galaxyproject/galaxy/issues/1881
>
> Greg Von Kuster
>
> On Apr 15, 2016, at 10:52 AM, Scott Szakonyi <scott.b.szakony...@nd.edu
> <mailto:scott.b.szakony...@nd.edu>> wrote:
&
Hi Daniel,
I'm a relative novice at Galaxy administration, but at first blush it looks
like you're missing (or the Galaxy user doesn't have permissions on) the
paste process. You can try a GIT status or diff to see if something just
didn't download right. Otherwise, check to make sure that your
quot; to the genome you need.
>
>
> Regards, Hans-Rudolf
>
> On 09/13/2016 09:11 PM, Scott Szakonyi wrote:
>
>> Hi all,
>>
>> I'm getting the following error when attempting to do a trackster
>> visualization:
>>
>> Error: The requested genom
Hi all,
I'm getting the following error when attempting to do a trackster
visualization:
Error: The requested genome file
(/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len)
could not be opened. Exiting!
Couldn't open /vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len
35 matches
Mail list logo
