To: Liisa Koski liisa.ko...@basf.com
Cc: galaxy-dev@lists.bx.psu.edu Dev galaxy-dev@lists.bx.psu.edu
Date: 11/04/2014 03:12 AM
Subject:Re: [galaxy-dev] trackster is not working on the
vrelease_2014.02.10--2--29ce93a13ac7
Hi Liisa,
For us, it was only copying the directory
Hello,
I am testing the example_watch_folder.py script on my local instance of
Galaxy (Feb.10 distribution). I have set up a simple workflow with the
Fasta-to-Tabular tool. It takes a single input fasta file. Works in Galaxy
UI.
I have created input and output folders and followed the steps
Hello,
I just updated to Feb.10 and also noticed that Trackster is not working. I
too get the blank screen. Could you please tell me how to manually update
the vis packed files? I do not know what these are.
Thanks in advance,
Liisa
___
:(
From: Dannon Baker dannon.ba...@gmail.com
To: Liisa Koski liisa.ko...@basf.com
Cc: Galaxy Dev galaxy-dev@lists.bx.psu.edu
Date: 13/03/2014 06:39 PM
Subject:Re: [galaxy-dev] Empty history pane
If it's possible, can you check (or ask the user to check) if there are
any
Our use was using the lastest Firefox release. I asked him to try FireFox
Portable and that seemed to do the trick. It was a problem with his
Firefox install.
Thanks for you help,
Liisa
From: Dannon Baker dannon.ba...@gmail.com
To: Liisa Koski liisa.ko...@basf.com
Cc: Galaxy Dev
Hello,
Our site maintains a local Galaxy installation (Nov.4th distributuion).
One of our usrers has lost the ability to view anything in his history
pane. He is able to run tools and view the list of 'Saved Histories' in
the middle pane but the History pane itself stays empty. When I
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered Users
per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
Thank you Jeremy,
It turned out the issue was our version of bedtools. We updated to 2.17.0
and no longer have the errors.
Cheers,
Liisa
From: Jeremy Goecks jeremy.goe...@emory.edu
To: Liisa Koski liisa.ko...@basf.com
Cc: galaxy-dev@lists.bx.psu.edu Galaxy-dev
galaxy-dev
Hello,
I created a simple workflow with an input file and the 'Select first'
tool. I wanted the value to be a parameter ${value}. I am able to save the
workflow and see the little grey parameters box at the top of the workflow
editor.
When I try to run this workflow I get a yellow box at the
Hi,
I'm running a local instance of Galaxy and no matter what tool I run I get
the following error:
Error executing tool: maximum recursion depth exceeded while calling a
Python object
In the log file:
galaxy.tools ERROR 2013-01-25 14:06:54,375 Exception caught while
attempting tool
Hello,
Can you please post the link to this patch? I do not see it in the mail
thread and I too have noticed some issues with the DRMAA job running since
updating to the Oct. 23rd distribution. I don't know if it is related yet
but I'd like to try the patch to see. I have two local instances of
Hi,
Can you please send the entire link to access this changeset? I keep
searching for 5013377e0bf7 but can not find it.
Thanks in advance,
Liisa
From: Dannon Baker dannonba...@me.com
To: Sanjarbek Hudaiberdiev hudai...@icgeb.org
Cc: galaxy-...@bx.psu.edu
Date: 13/11/2012 12:34
That did it! Thanks Nate!
From: Nate Coraor n...@bx.psu.edu
To: Liisa Koski liisa.ko...@basf.com
Cc: galaxy-dev@lists.bx.psu.edu
Date: 12/11/2012 12:13 PM
Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py
On Nov 8, 2012, at 8:55 PM, Liisa Koski wrote:
Hi
Hello,
I've installed a tool to my local Galaxy installation via my local
ToolShed. I would like to run this tool locally, and not have it submitted
to the grid.
I have tried two ids in the universe_wsgi.ini [galaxy:tool_runners]
section.
The tool id directly from the tool.xml file and the id
Hello,
I'm trying to create a custom visualization in Trackster. I am doing the
following steps. Visualization - New Visualization - Add a Custom Build
I get directed to the url below:
http://galaxy.ca:8080/user/dbkeys?use_panels=True
But the web page says:
Server Error
An error occurred. See
Cock p.j.a.c...@googlemail.com
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Cc: Liisa Koski liisa.ko...@basf.com
Date: 26/09/2012 04:33 AM
Subject:Re: [galaxy-dev] problem installing blast_datatypes
manually
On Tue, Sep 25, 2012 at 8:39 PM, Peter Cock p.j.a.c
Hello,
I followed the instructions below to manually install the blast_datatypes:
Manual Installation
===
Normally you would install this via the Galaxy ToolShed, which would move
the provided blast.py file into a suitable location and process the
datatypes_conf.xml entry to be
Hello,
I am trying to run the cleanup scripts on my local installation but get
stuck when trying to run the following:
./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5
-r
Deleting library dataset id 7225
Traceback (most recent call last):
File
Hello,
After updating to the Sept. 07 distribution I am having problems editing
an existing workflow.
Server error
URL:
http:galaxy_url/workflow/load_workflow?id=ba751ee0539fff04_=1348501448807
Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ,
Hello,
I get an error when trying to upgrade my mysql db with sh manage_db.sh
upgrade from version 94-95 (see below).
Will cause problems with my installation?
sh manage_db.sh upgrade
93 - 94...
Migration script to create handler column in job table.
done
94 - 95...
Migration script to
Hello,
I cloned a workflow on my local Galaxy installation, renamed it, made some
edits and pressed save. It has been saving now for about 3 hours. It only
has 12 steps.
Any suggestions?
Thanks in advance,
Liisa
___
Please keep all
Hello,
I'm seeing some discrepancies in total user usage versus what my histories
actually total so I wanted to run set_dataset_sizes.py and
set_user_disk_usage.py
I am getting the following error.
./set_dataset_sizes.py
Loading Galaxy model...
Processing 77915 datasets...
Completed 0%
Hi Dannon,
Yes...the tags have piled up. I will apply this fix and try to remove some
of the existing tags.
Thanks for your suggestion.
Liisa
From: Dannon Baker dannonba...@me.com
To: Liisa Koski liisa.ko...@dnalandmarks.ca
Cc: galaxy-dev@lists.bx.psu.edu
Date: 21/03/2012 09:08
Hi,
I have tried running (on my local instance) a number of tools
(fasta_to_tabular, tandem_repeat_finder, others) on my fasta file but keep
getting the error Error executing tool: 'fasta' after file execution. In
the log file I see this
10.1.1.119 - - [27/Jan/2012:15:47:15 -0400] GET
Hello,
I am trying to upload BAM files (by pasting a URL) to my history(or
DataLibrary) and get the following error. These are bam files which I had
previously uploaded with no problems.
Traceback (most recent call last):
File /doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py,
Hi,
I'm trying to upload data to Data Libraries from filesystems paths as
Admin. I get the following error.
Any ideas?
Thanks in advance,
Liisa
Traceback (most recent call last): File
/data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in
__main__() File
Hi Peter,
Thanks! The fix worked with the new Illumina format.
Your help is much appreciated :)
Cheers,
Liisa
Liisa Koski
Bioinformatics Programmer
From:
Peter Cock p.j.a.c...@googlemail.com
To:
Liisa Koski liisa.ko...@dnalandmarks.ca
Cc:
galaxy-dev galaxy-...@bx.psu.edu
Date:
2011-12-12
Hi ,
Looks like the tool Divide FASTQ file into paired and unpaired reads is
not recognizing my paired-end naming suffix
@HWI-ST916:79:D04M5ACXX:1:1101:1:100326 1:N:0:TGNCCA
@HWI-ST916:79:D04M5ACXX:1:1101:1:100326 2:N:0:TGNCCA
Is there a patch for this or another tool/way I can divide
Thanks Jeremy, that changeset fixed the issue :)
Cheers,
Liisa
From:
Jeremy Goecks jeremy.goe...@emory.edu
To:
Liisa Koski liisa.ko...@dnalandmarks.ca
Cc:
galaxy-dev@lists.bx.psu.edu
Date:
2011-11-30 18:07
Subject:
Re: [galaxy-dev] Can't view data files from published histories, only
Hi,
I lost my Data Libraries when I updated to the latest galaxy-dist release
:( What would be the best way to go about getting them back?
Thanks in advance,
Liisa
___
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in your mail
Sorry! They are back! I was looking at the wrong installation :(
Thanks,
Liisa
From:
Greg Von Kuster g...@bx.psu.edu
To:
Liisa Koski liisa.ko...@dnalandmarks.ca
Cc:
galaxy-dev galaxy-...@bx.psu.edu
Date:
2011-11-30 13:45
Subject:
Re: [galaxy-dev] Lost my Data Libraries when I updated
,
Liisa
Liisa Koski
Bioinformatics Programmer
Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca
Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec
CANADA
DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science
company
Confidentiality notice
Hi Jeremy,
I'm trying to view boxplots (png) and FastQC (html) output. I can view
other output types like tabular in the published histories, but not png or
html.
Thanks,
Liisa
Liisa Koski
Bioinformatics Programmer
Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca
Postal Address: DNA
Hello,
I noticed a change in the newest version. When importing Library Datasets
into Histories...if you enter a New History name for the destination
Galaxy will import into the new AND current history. So it is getting
imported into two histories. Is this a bug? It would really be nice to
Hi,
I'm trying to grab data from my local custom BioMart and export it to my
local Galaxy installation. I did this by changing the address in the
biomart.xml file
inputs action=http://mydomain/biomart/martview; check_values=false
method=get target=_top
displaygo to BioMart
Is it possible to run a specific workflow only on certain nodes of the
cluster? Either using the API or by setting something in the config files?
Thanks,
Liisa
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in your mail client.
Hi,
Yesterday I ran the cleanup_datasets.py scripts as follows..
Deleting Userless Histories
python cleanup_datasets.py universe_wsgi.ini -d 10 -1
Purging Deleted Histories
python cleanup_datasets.py universe_wsgi.ini -d 10 -2 -r
Purging Deleted Datasets
python cleanup_datasets.py
Hello,
I have a local instance of galaxy and after successfully running an NGS
analysis I am trying to save my BAM file to my local machine. When I click
on the save icon my Galaxy instance crashes with the following error. This
also happens when I try to save the SAM file. It does not happen
Thanks Nate! I set 'debug = False'and now I have no problem downloading my
BAM/SAM files.
Cheers,
Liisa
From:
Nate Coraor n...@bx.psu.edu
To:
Liisa Koski liisa.ko...@dnalandmarks.ca
Cc:
galaxy-...@bx.psu.edu
Date:
2011-03-22 12:06
Subject:
Re: [galaxy-dev] Can't save BAM file from Galaxy
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