Hi guys,
I wasn't sure if I should send this one to galaxy-user. I have just
confused myself about the versions of tools displayed within Galaxy.
If I select the TopHat tool, the tool UI says Tophat for Illumina
(version 1.5.0).
After I have run the job, the step panel in the History window says
On Monday, December 10, 2012, Jeremy Goecks wrote:
Decompress and unpack the file and you'll find the relevant files (though
everything now has extensions with p* rather than n*); add an entry to
blastdb pointing to the directory with these files and you should be good
to go.
J.
Not
This has been confusing for me also. Perhaps if we had a way to
distinguish between
the two by prefixing the tool version of a wrapper with w0.0.5 and the
actual tool version with v1.3.0?
I think that Galaxy determines the versions of the tools it loads at
startup in lib/galaxy/tools/__init__.py
Hi all,
I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer
seems do not reganize the name of the pair-end reads, and treat the pair-end
reads as non-pair-edn reads.
Best regards___
Please keep all replies on the
Hi,
I have been using the tool shed recently and come across a problem.
When a searching for valid tools within the Public Tool Shed, it seems that if
the search should return nothing found, it is instead displaying a Server Error
page instead.
For example:
Hello,
One of my users gets the following message when he wishes to edit the
attribute of a dataset which is generated by using a tool (same problem
as it is a tool provided by Galaxy or a tool coded by us).
Do you have any idea?
Thanks in advance,
Sarah Maman
URL:
Hello,
For one of my tools that I have added to my local instance of Galaxy, I
can not add this tool in the editing workflow. When I click on the tool
name in the tools windows on the left, it does not appear in the
editing workflow.
Do you have any idea?
Thank you in advance,
Sarah Maman
Hi, Dannon.
Thanks for the tip. No, I was not reusing the cluster names exactly to
avoid previous data to mess up with my fresh new deployments. There were indeed
about 8 buckets referring to clusters that don`t exist anymore. Write now I
can`t remove my current cluster by the
Thx Hans-Rudolf
But I did write /output in the xml file
Here is just a mistake
In ~in ~/database/files/ folder there is just a folder named 000
and there are lots of *.dat file in 000 folder
From: Hans-Rudolf Hotz h...@fmi.ch
To: Chenhao
Thanks Danon,
But I have no error generated in my error log file (logs of run.sh):
[11/Dec/2012:16:39:09 +0200] GET /galaxy/workflow HTTP/1.1 200 -
http://URL/galaxy/root; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0)
Gecko/20100101 Firefox/17.0
IP - - [11/Dec/2012:16:39:11 +0200] GET
The paster.log is just the file for the output you've copied below when running
daemonized -- if you're running in the foreground it just gets sent there
instead of to the file. So, no obvious errors there. Could you check for
javascript console errors?
And, if you'd like, feel free to send
Dannon,
Here is myjavascript console errors :
SyntaxError: missing ) after argument list :
/*
ool( 'sm_miRNA_join_annot', '* Construction de la matrice d'annotations' )
*/
/*editor...8829fc# (ligne 1, col. 60)*/
I replaced this syntax Construction de la matrice d'annotations by the
latter
Hi,
I am trying to look mutations/SNPs in RNA-Seq data. Can anyone suggest me a
workflow in Galaxy on how to detect SNPs and mutations
Thanks in advance
Suz
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Hi,
Is it possible to download a dataset when require_login=True in
universe_wsgi.ini using the API key?
Thanks,
Ilya
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Hi guys,
I tried the impersonate a user feature, but I don't know how to stop
impersonating a user?
I tried going back to the impersonate a user feature and selecting
myself but it's not clear if it changed anything, and I no longer see
the History items I had before I did the impersonation.
Hi Franco,
I'm not quite sure what page you'r eon, but if you're looking at the page that
has the tool dependency with the error status, you should be able to click the
link of the tool dependency and see the error, log, etc. If this is not the
page you're referring to, then I'll have to take
Hi all,
I have a pipeline involving a series of scripts, which creates
directories (and many subdirectories), that I'd like to wrap for use in
Galaxy. Although the contents of the folders are not the primary output
of the pipeline, (and I don't want them as history items), I'd still
like them
Hi Nate,
I loaded the file named s_6_1_sequence.txt.gz (Illumni file) under the login
name abdul.ban...@uconn.edumailto:abdul.ban...@uconn.edu as FTP.ftp://ftp.R
Whenever I am trying to load it as history so that I can run it for analysis,
the file upload is showing error and massage comes
Hi Greg,
Try clicking the logout button. That should logout of the user you are
impersonating and back into you. Although, this does have a few quirks also
and may log you right out. Don't forget that when you are impersonating
someone the history may not be automatically loaded and you will have
Hi all,
I could use some help getting DMRAA to run. We already have a galaxy instance
with pbs running, but I'd like to connect to Torque using dmraa because we
eventually intend to port over to a different resource manager.
I've followed these instructions:
I have a local galaxy server, and I built a workflow, it got stuck in one
step in the middle. The computer is a 64 cores server, and no other jobs
running in this server.
Any idea how to trouble shooting?
Thanks,
Fenglou
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有olb吃掉
Yunbo Xu
817 Hickman rd, Apt A-23
Augusta,GA 30904
706 - 877 3892
On Dec 11, 2012, at 4:13 PM, Lei Yan leiyan2...@gmail.com wrote:
Dear Dannon and James,
On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker dannonba...@me.com wrote:
• I installed a Cloud Galaxy instance one month
Hi list,
I got the following tool_dependencies.xml file failing:
?xml version=1.0?
tool_dependency
package name=bedtools version=2.17.0
install version=1.0
actions
action type=download_by_url target_filename=bedtools-2.17.0.tar.
gz
Franco,
BEDTools, unlike some other packages, does not require the 'make clean'
shell command to compile. If you remove that line, the dependency should
install without problems.
--Dave B.
On 2012-12-11 21:16, Franco Caramia wrote:
Hi list,
I got the following tool_dependencies.xml file
Hi list,
We have found that, in Galaxy, when we add dataset to a library under
Manage data libraries, Galaxy sometimes detects the type of the file and
sometimes does not. What I have noticed is that it detects the type of the
file when we select Copy file into Galaxy under Copy data into Galaxy?
Hi all,
We are trying to get our instance of Galaxy submitting jobs to a cluster a
using the staged method referred to at
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Our cluster is
running Torque 4.1.3. We need to use Torque 4.x clients to be able to submit
jobs to it.
Franco,
You're right, I see a both clean and all rules in the makefile. It looks
almost like it's not finding the expected makefile, I'll have to look
into that in the morning. As for the download_by_url action, it
downloads and extracts the specified file, then changes to the extracted
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