Mic;
(moving to galaxy-dev list so folks there can follow, but future
questions are more appropriate for the Biopython list only since
this isn't a Galaxy question)
I have the following GFF file from a SNAP
X1 SNAPEinit 25792712-3.221 + . X1-snap.1
[...]
With
On Wed, May 1, 2013 at 11:43 AM, Mike Dyall-Smith
mike.dyallsm...@gmail.com wrote:
Hi Peter,
In biolinux, I start galaxy by a clicking on an application icon.
If I open the terminal and run the suggested command: $ sh run.sh | grep -i
blast
I get the following output (long):
$ sudo sh
Hi Greg Dave,
I really like the new features on the (Test) Tool Shed for searching
my repositories:
* Latest revision missing tool tests
* Latest revision failing tool tests
* Latest revision all tool tests pass
However there are some teething problems. Some of my tools are
listed under Latest
Hi Peter,
OK, I've worked out why the terminal did not start up galaxy. I have done
that, performed a blastp search, and it failed with the usual error, but
now I have the terminal output for that failure.
Firstly the error report from galaxy:
On Wed, May 1, 2013 at 12:09 PM, Mike Dyall-Smith
mike.dyallsm...@gmail.com wrote:
Hi Peter,
OK, I've worked out why the terminal did not start up galaxy. I have done
that, performed a blastp search, and it failed with the usual error, but now
I have the terminal output for that failure.
On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote:
1) Any idea which proxy settings in the universe_wsgi file need to be set
other than the ones on the website? Those are the only ones I changed. I
scrolled down to the 'Advanced Proxy' settings but didn't see anything that
looked relevant
Hi All,
I have installed snpEff 3.1 from the galaxy toolshed into my cloud man
instance. The tool runs to completion, but I get an empty file. It says as
'no peek' in the history. When I view the details and check the stderr and get
the following:
WARNING: Chromosome '@PG' not found. File
=VCFv4.1
##fileDate=20130501
##source=freeBayes version 0.9.6
##reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
##phasing=none
##commandline=freebayes --bam localbam_0.bam --fasta-reference
/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa --vcf
/mnt/galaxyData/files/000/dataset_101
Hi Peter,
I created the following Trello card for this and things will be fixed as a
priority. Thanks for letting us know!
https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823
On May 1, 2013, at 7:09 AM, Peter Cock wrote:
Hi Greg Dave,
I
Hello Mattias,
I've created the following Trello card for this and we'll get it fixed asap.
Thanks for letting us know.
https://trello.com/card/toolshed-unable-to-download-repositories-as-zipped-archives/506338ce32ae458f6d15e4b3/824
Greg Von Kuster
On Apr 29, 2013, at 3:35 AM, Hollander,
Mattias,
Thank you for reporting this error, the issue has been resolved, and
downloading zipped files from the main tool shed is working.
--Dave B.
On 5/1/13 08:55:50.000, Greg Von Kuster wrote:
Hello Mattias,
I've created the following Trello card for this and we'll get it fixed asap.
Thanks for fixing!
On 05/01/2013 04:29 PM, Dave Bouvier wrote:
Mattias,
Thank you for reporting this error, the issue has been resolved, and
downloading zipped files from the main tool shed is working.
--Dave B.
On 5/1/13 08:55:50.000, Greg Von Kuster wrote:
Hello Mattias,
I've
##fileformat=VCFv4.1
##fileDate=20130501 ##source=freeBayes version 0.9.6
##reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
##phasing=none ##commandline=freebayes --bam localbam_0.bam
--fasta-reference /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
--vcf /mnt/galaxyData
Format data
##fileformat=VCFv4.1
##fileDate=20130501
##source=freeBayes version 0.9.6
##reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
##phasing=none
##commandline=freebayes --bam localbam_0.bam --fasta-reference
/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa --vcf
/mnt
the following error: unable to find FASTA index
entry for '1'. The
resulting files is:
ChromPos ID Ref Alt QualFilter InfoFormat
data
##fileformat=VCFv4.1
##fileDate=20130501
##source=freeBayes version 0.9.6
##reference=/mnt/galaxyIndices/genomes
In the Apache access.log, a single access link results in a great many
output lines; the first two look like this:
128.233.109.35 - - [01/May/2013:14:31:29 -0600] GET /galaxy HTTP/1.1 200
5058 - Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5)
AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4
Peter,
Thanks for the data, I am in the process of tracking down the source of
the issue, and I hope to have a fix ready shortly.
--Dave B.
On 2013-05-01 08:52, Greg Von Kuster wrote:
Hi Peter,
I created the following Trello card for this and things will be fixed as a
priority. Thanks
Hi Kim,
The main public Galaxy server is very busy right now. Also, this message
usually occurs when a user is doing something at the exact moment when
the server is at a certain stages during an update (we did one
yesterday). Sorry if this was confusing!
When you say that the job never
Hi Peter,
Standardized Repository Actions menu in the tool shed is available in changeset
revision 9555:fadc4b334f3e which is currently running on the test tool shed.
Thanks for your request!
Greg Von Kuster
On Apr 25, 2013, at 5:13 AM, Peter Cock wrote:
Hi all,
This is just a usability
Hi all,
I'm Venice and I'm new in Galaxy. I installed a local Galaxy and I just
want to know how I can output to history an external file stored outside my
galaxy-dist folder. I created an xml explicitly stating the absolute path,
but when I run the tool, it says Either this dataset does not
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