I think this is great. Do we have it clearly explained on the wiki somewhere
about how to turn on mailing list mode within biostar? I didn’t see anything in
a quick search, but it would probably help ease the transition for people that
just love the mailing list approach. I also find it
.
Regards,
Kaz
2014-04-12 13:08 GMT+09:00 Daniel Blankenberg d...@bx.psu.edu:
Hi Kaz,
We do have a problem with the Table Recalibration tool on Main right now.
We'll let you know when we have a fix.
Thanks for using Galaxy,
Dan
On Apr 11, 2014, at 10:24 PM, KS k...@kyudai.jp wrote
Hi Kaz,
We do have a problem with the Table Recalibration tool on Main right now. We’ll
let you know when we have a fix.
Thanks for using Galaxy,
Dan
On Apr 11, 2014, at 10:24 PM, KS k...@kyudai.jp wrote:
Hi Bjoern,
Thank you for the reply.
I found Table Recalibration, probably from
Hi Nishant,
In your universe_wsgi.ini file, you need to set:
allow_user_dataset_purge = True
Thanks for using Galaxy,
Dan
On Apr 10, 2014, at 8:09 AM, Nishant THAKUR tha...@ciml.univ-mrs.fr wrote:
Hello,
I am using local galaxy server. I have disc storage problem and I noticed
that
Hi Casey,
I was able to confirm this issue and we’ll work on a fix for it. Thanks for
reporting.
Thanks for using Galaxy,
Dan
On Feb 6, 2014, at 10:25 AM, Jennifer Jackson j...@bx.psu.edu wrote:
Hi Casey,
I just tested the UI unsharing for both of your cases and was unable to
Hey Mo,
You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to
create your instance, it should display an example connection string that will
work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem
ubuntu@IP', after your instance launched.
Once
Hi Eduardo,
I've committed some code that should fix the issue that you are experiencing,
and it will be available on the main server after the next update (some time
next week).
Until then, if you change the name of e.g. your history item 34 to not have a
'í' or other non-ascii characters
Hi Chunyu,
Thanks for reporting this issue, it has been resolved in our stable branch and
will be available on our public server after the next update.
Thanks for using Galaxy,
Dan
On May 12, 2013, at 10:52 AM, Chunyu Liu wrote:
hi,
I had an odd problem today, seems not a problem
Hi Gema,
For example, see the Combine FASTA and QUAL into FASTQ tool for creating a
FASTQ file from FASTA data; when quality data is not provided, fake score
values will be used.
Thanks for using Galaxy,
Dan
On Apr 3, 2013, at 10:42 AM, Peter Cock wrote:
On Wed, Apr 3, 2013 at 3:40
Hi Aaron,
I just tested this small example and it reported one region as the result of
the intersect:
https://main.g2.bx.psu.edu/u/dan/h/aaron-quinlan-intersect-test-02-08-2013
Do you have a history available that you can share (privately if you desire)
where you see the issue, and we'll take
zero intersections. Join, in contrast, works fine. I'd
be happy to share the files. Would it be best to send them directly to you
by email? The are small.
Thanks much for the help,
- Aaron
quinlanlab.org
On Feb 8, 2013, at 2:56 PM, Daniel Blankenberg d...@bx.psu.edu wrote
Hi Anna,
Thank you for reporting this error. There is currently an issue with displaying
the link in the history item for the way we normally display interval datasets
at UCSC.
However, we have an alternative method available and I have enabled that for
now. You will need to refresh the
Hi Umar,
Can you click the eye icon to view the contents of the 'log' dataset for the
GATK run. The end of the log should have the actual error encountered (the text
you provided is a bit of a red herring)
Since you are using hg19, the most likely cause for the error is that the
reference
Hi Philippe,
The GATK wrappers provided with the Galaxy distribution are for GATK version
1.4. There is a set of 1.6/GATK-lite wrappers that has been developed by the
team, but is not yet available. There may also be other options available in
the Tool Shed that have been contributed by the
Hi Joshua,
Is this on the main public site? If so, can you share your history with me and
I'll take a look? If this is on a local instance, can you provide additional
information, such as the GATK version that you are using?
Thanks for using Galaxy,
Dan
On Dec 11, 2012, at 5:34 PM, Joshua
Hi Rolando,
You'll need to remove the old blast datatypes from your datatypes_conf.xml
file. If you haven't added any new datatypes manually yourself, you can copy
the datatypes_conf.xml.sample file over of your datatypes_conf.xml file.
Also, in the future questions about local Galaxy
Hi Chris,
Are you able to share a copy of the offending file? Perhaps by uploading to the
public Galaxy server, possibly trying the Grooming step there, and then sharing
the history with me or by using the bug report option on the Grooming step if
it fails?
If not, you could look at the
Hello,
Thanks for reporting this error. This has been fixed in changesets
7875:62b89df24ab1 through 7879:046634d05007 in galaxy-central and will be
included in the next distribution and main update. Please let us know if you
encounter additional issues after the update.
Thanks for using
Hi Di,
You need to remove the starting comment/hash from the admin_users line:
admin_users = dkngu...@uw.edu
Thanks for using Galaxy,
Dan
On Jul 20, 2012, at 5:13 PM, Di Nguyen wrote:
Dear all,
Please help me figure out what went wrong to set up ADMIN in my local
instance using the
://www.bx.psu.edu/hg/galaxy/ (mentioned in NewsBrief website). I use the
first one to update Galaxy. I tried to pull the below changeset, but it says
'invalid revision'.
Please suggest.
Best,
Raj
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Thursday, March 01, 2012 8:45
Hi Raj,
Thanks for reporting, this issue has been resolved in changeset
6778:35be930b21be. Please let us know if you encounter further issues.
Thanks for using Galaxy,
Dan
On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote:
Hello,
I'm facing an issue with Depth Of Coverage tool
Hi AP,
Please keep all replies on list, this will allow the community to assist and
benefit from these correspondences.
SICER requires BED input. To go from BAM to BED:
1.) Convert BAM to SAM
2.) Convert SAM to Interval (Convert SAM to interval)
3.) Convert interval to BED(6+). This can be
Hi AP,
SICER requires BED formatted input with at least 6 columns (for strand
information). You can convert your BAM files into SAM and then into interval
and BED format. Once you have your input in the BED (6+) format, you should be
able to use these tools. Please let us know if we can
Hi Rahul,
This is the maximum number of bases which can have their score not included
when calculating the result of the selected aggregation function.
For example, if you had a 5 base window with scores of 5,5,2,5 and 5, set
aggregation to min score with a specified value of 4, with the
Hi Franzi,
You have one too many hg19 in there. The fields go like:
unique_build_id dbkey display_name fasta_file_path
valid_tool_suites
so:
hg19hg19hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa
gatk
But do note that these tool integrations are still
Hi Steffi,
GeneTrack should be working again on the Main server, thanks for reporting the
error.
For information on the inner workings of GeneTrack, you should consult the
paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you can
additionally contact the GeneTrack author,
analysis: 19,
20 and 21 cover the usage and principles of GeneTrack (among other
topics)
http://bcc.bx.psu.edu/courses/597D-2011/index-597D-2011.html
best regards,
Istvan
On Thu, Nov 10, 2011 at 12:19 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Steffi,
GeneTrack should be working
Hi Uwe,
Multiple selects for dataset inputs is not yet supported, but there is a ticket
open on this issue, which you may follow if you like:
https://bitbucket.org/galaxy/galaxy-central/issue/137/allow-multiple-true-in-input-param-fields
We have not yet decided when-or-if we will be
Hi Amit,
Without taking a look at your history, I'll have to make a guess. When you
retrieve regions from UCSC, on the second step, right before you click Send
query to Galaxy, make sure that you have Whole Gene selected under One
record per, and that you are looking at a gene track and that
Hi Florent,
Sorry for the delay. I did try the patch out shortly after you contributed it,
but it caused the functional to fail. I was able to fix the issue and allow
the existing tests to start passing, but I've been bogged down lately and
haven't been able to perform a more thorough review
Hi Prashant,
Have you set:
use_debug = False
use_interactive = False
In your universe_wsgi.ini file?
Thanks for using Galaxy,
Dan
On Oct 17, 2011, at 6:15 PM, prashant singh wrote:
Hi
We have installed Galaxy on a local machine (Mac pro 2 x 2.4 gHz quad
core Intel Xeon with 32 GB RAM).
Hi Shambhavi,
It sounds like your tool_conf.xml file is malformed. Check that you have
proper quotes and that the tag open and close are all correct, etc. There are
several programs out there that can validate xml files for you, you may wish to
try to validate your xml file with one of those.
Hi Rad, Jorge,
Sorry for the delay in reply. We have not yet released a pre-canned workflow
to do this. However, if you are looking to associate one set of Genomic
interval/region data with another set, Galaxy's interval operation tools are a
good place to begin. There are good examples of
Hi Rich,
Sorry for the delay in reply. You can configure the display of custom tracks at
UCSC by clicking on the custom track within the UCSC genome browser. You can
also convert your wig file to a bigwig file (under Convert Formats tool menu),
in order to speed up the display of this data.
Hi Tania,
In the History pane, Click 'Options' -- 'Saved Histories' and see if your
history is listed there.
Thanks for using Galaxy,
Dan
On Mar 24, 2011, at 12:15 PM, Fuchs, Tania wrote:
Hello,
I worked on my home computer with Galaxy online and next day when I came to
the lab I
Hi David,
Your files appear to be of the Sanger FASTQ variant. As you have noticed, the
info blurb provided by the Grooming tool provides information that should be
utilized to confirm input types. While the 'Illumina 1.3+' FASTQ format does
encode scores using a different ASCII range, it is
Hi Karl,
Using the upload tool for https URLs was added in changeset 5220:425076fe5ea0.
I am not sure when this will make it to the Cloud image, but meanwhile, if you
can access the file without using ssl (just 'http'), you should be able to
upload. If this is not the issue you are
Hi Sylvain,
This issue has been fixed in changeset 5207:72d560d3e7fd and will be available
the next time that the main server is updated, which should be within the next
few weeks. Thanks for reporting this error and please let us know if we can
provide additional assistance.
Thanks for
Hi Stephen and Peter,
This change is definitely possible, and because the SAM format specifies that
its quality scores are phred scaled and ASCII offset of 33 (regardless of
provided input) it shouldn't cause complications downstream. We'll add this to
our todo list. I created a ticket:
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