Galaxy 2.2 is down
by Ross Hardison
None of the Galaxy servers except Galaxy1 and Galaxy cluster are
responding.
- Ross
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8(a)psu.edu
phone: 814-863-0113 FAX: 814-863-7024
14 years, 3 months
Proxy Error Message
by Stephanie Justice
When I tried to use Galaxy 2.2 I received the following message around 2 pm
on October 15, 2006:
Proxy Error
The proxy server received an invaild response from an upstream server.
The proxy server could not handle the request *GET/.*
**
Reason: Error reading from remote server.
I am using Verizon DSL to access via Microsoft Explorer. I have tried to
access Galaxy since 10 pm last night without success or this error message
until now. The page would just refresh and say done at the bottom.
Hope this helps.
Stephanie Justice-Bitner
Penn State Hershey Grad Student
14 years, 3 months
Tools: Operate on Genomic Intervals: Merge
by Erika
Dear Galaxy Help,
I was wondering if it would be possible to get the coordinates that
caused the merge as the output from "Tools: Operate on Genomic
Intervals: Merge the overlapping intervals of a query", rather than
the entire merged interval as the output. Kind of like the output
from "Intersect: Overlapping Pieces of intervals" option, which
returns the exact base pair overlap between two queries. It might be
helpful in some cases to see only the coordinates that caused the
merge. From my limited Galaxy knowledge, by using the "Intersect"
option and comparing a file to itself, the output would also include
those complete overlaps of interval_1 in file1 to it's copy
interval_1 in file2. If there is already a way to get just the
coordinates that caused the merge, I would be interested to learn more.
Thanks again for your help!
- Erika
**********************************************************
E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185
kvik(a)bx.psu.edu
14 years, 3 months
error message when importing GC content
by Ross Hardison
When I use the Table Browser proxy in Galaxy to import data on "GC
content in 5bp intervals", I get the data I want (in wiggle format).
However, the information associated with the query in Galaxy says:
3: UCSC: gc5Base (chr16:1-500000)
error, format: wig, database: hg17
Info: Errors: (line
100010)-----------------------------------------------------------------
---------- (line
100013)-----------------------------------------------------------------
---------- <br>UCSC: gc5Base (chr16:1-500000)
As far as I can tell, the data are there and are OK (it converts from
wiggle to BED OK, and the expected 100,000 lines are present).
It is disconcerting to users to get the error message.
Thanks,
Ross
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8(a)psu.edu
phone: 814-863-0113 FAX: 814-863-7024
14 years, 3 months
Galaxy screencasts
by Cathy Riemer
Hi Nate,
I'm having trouble viewing the Galaxy screencasts with my
Ubuntu workstation and Firefox. The default app for playing
.mov files is "Movie Player" which turns out to be Totem,
but I get the following error message:
Totem could not play 'file:///tmp/InterFace.mov'.
You do not have a decoder installed to handle this file.
You might need to install the necessary plugins.
It is not entirely clear which of the gstreamer plugins
packages is needed for this content.
Too bad Apple doesn't have a Quicktime version for Linux. :-(
-Cathy
14 years, 3 months
share items between histories
by Julien Lagarde
Hi Anton or whoever else in the Galaxy,
is it possible to share (or directly copy) items between different
histories in galaxy? if not this would be very helpful i think.
cheers
j
--
-----------------------------------------------------
Julien Lagarde
Genome Bioinformatics Research Group
Centre de Regulacio Genomica
Grup de Recerca en Informatica Biomedica (IMIM)
Dr. Aiguader, 88 (+34) 93 3160170 ph
E-08003 Barcelona (+34) 93 3160099 fax
http://genome.imim.es/~jlagarde/
--------------------------------
14 years, 3 months
history has 100 jobs i did not process/do not recognize
by Erika
hi,
i was using galaxy earlier today. i came back from maybe 2hrs break
and now my history has about 100 jobs i do not recognize. and i do
not see my jobs in this list. unfortunately, i was not logged on as
a user. this is the link i get if i click on "history options: share
current history". is this someone else's history? can mine be
retrieved by any chance?
thanks,
erika
http://main.g2.bx.psu.edu/history_import?id=263
**********************************************************
E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185
kvik(a)bx.psu.edu
14 years, 3 months
