Jobs deleted staying in 'dr' status
by Mathieu Bahin
Hi all,
We have been developing our own Galaxy instance for a while now. We have a cluster on which the job are sent to be executed, it is managed through SGE. Usually, communication between SGE and DRMAA is ok and we don't have any problem with that.
When a job is deleted by the user, most of the times, the job disappears but sometimes, we don't know why, the job stays and has the status 'dr' within SGE. If we don't kill it 'manually', it stays forever. It is not always the same tools which produces this error .
Have you any idea why how manage it ?
We have another problem, a display one.
Since the last update, we experienced problem with the history. Launching a job, it was very long to appear in the history and we had to refresh.
We got a more recent version of firefox and it seems that we don't have the problem anymore. But some user of ours can't update their firefox. Are you aware of that problem ?
Cheers,
Genouest Platform, Rennes - FRANCE
8 years, 9 months
Error running workflow via API
by John Eppley
The API interface is translating my parameters into python repr strings instead of actual strings.
A command that should look like this:
createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NNNNNN NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20664.dat
is getting run as this:
createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NNNNNN > /slipstream/galaxy/production/data/files/020/dataset_20728.dat
The input table in the tool info page is:
Input Parameter Value Note for rerun
chemistry type: <galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10>
First barcode NNNNNN
Second (optional) barcode NNNNNN
I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet.
Thanks
-john
8 years, 9 months
Launching a workflow via API, multiple params for one tool
by John Marmaduke Eppley
As far as I can figure out, the parameter map for running a workflow via the API is supposed to look like this:
{'blastn': {'param': 'evalue', 'value': '1e-06’}}
This doesn’t seem to allow for multiple parameters to a single tool. Is there a way to submit multiple parameters that I’m missing? For example:
{'blastn': {'param': 'evalue', 'value': '1e-06’, 'param': ‘identity_cutoff’, ‘value’: ’70’}}
…will not work. The dict() container doesn’t allow duplicate keys, it just overwrites the values.
Thanks
-john
8 years, 9 months
jobs stuck in new state
by David Hoover
I have many jobs stuck in the 'new' state on our local Galaxy instance. The jobs can't be stopped using the Admin->Manage jobs tool. First, does anyone know why a job would get stuck in the 'new' state for weeks? I have cleaned things up by manually setting their states to 'error' in the MySQL database. Is there a better way of dealing with 'new' jobs?
BTW, our Galaxy instance was updated about two weeks ago.
Wondering,
David Hoover
Helix Systems Staff
8 years, 9 months
Error getting Detrprok_wf working on local Galaxy instance
by Bernardo Bello
Hi,
While problems are been solved in my other Galaxy instance (MAC OSX), I
tried to install Galaxy on local Linux machine running Ubuntu 12.04.
Surprisingly, seems I have been able to get Galaxy toolshed work. The
problem I have now is that I'm trying to run a published workflow, named '
Detrprok_wf <http://127.0.0.1:8080/workflow/run?id=f597429621d6eb2b>', that
requires S-Mart installed and Detrprok scripts installed. Both of them
are installed, however although I've also been able to import the
corresponding wokflow 'Detrprok_wf', seems there is something wrong. See
attached files.
https://drive.google.com/file/d/0B8-ZAuZe8jldNE5ncktjTFZ6SG8/edit?usp=sha...
https://drive.google.com/file/d/0B8-ZAuZe8jldbTVxTTM3Ujluems/edit?usp=sha...
Thanks for your help, Bernardo
Command and actions up to now:
python --version
hg clone -v https://bitbucket.org/galaxy/galaxy-dist/
cd galaxy-dist
hg update stable
sh run.sh
#7. Workflow installation instructions
#The workflow should be run on a local Galaxy instance or one hosted on a
distant server. Refer to the tutorial (
http://wiki.galaxyproject.org/Admin/Get_Galaxy) for creation of a #Galaxy
instance. As the workflow has several steps running in parallel, the Galaxy
instance should use a database management system supporting concurential
access such as #postgreSQL, instead of the default SQLite system. The
DETR'PROK pipeline is obtained from the Galaxy main tool shed (
http://toolshed.g2.bx.psu.edu/), or my experiment (http://#
www.myexperiment.org), searching by name "detrprok_wf", and should be
installed by the Galaxy instance administrator. DETR'PROK requires
installation of the S-MART toolbox [13] and 3the "detrprok_scripts", both
available in the Galaxy main tool shed.
done # replace admin = none by admin = popnard(a)gmail.com in
'universe_wsgi.ini' file
lets see if this is not essential # postgreSQL installation (
https://help.ubuntu.com/community/PostgreSQL)
done # The DETR'PROK pipeline is obtained from the Galaxy main tool shed (
http://toolshed.g2.bx.psu.edu/
done ## DETR'PROK requires installation of the S-MART toolbox [13] and the
"detrprok_scripts"
# S-MART needs the folowing packages
R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in%
rownames(installed.packages()) == FALSE){install.packages("RColorBrewer",
repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in%
rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos =
c("http://cran.rstudio.com/"), dependencies = TRUE)}'
# set 'tool_dependency_dir'
mkdir tool_dependency_dir
# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
tool_dependency_dir = /home/usuario/tool_dependency_dir
# install 'detrprok_wf' nad from 'repository actions' import workflow to
Galaxy
NOTE -> Workflow Detrprok_wf imported successfully. The following tools
required by this workflow are missing from this Galaxy instance: name:
bam_to_sam, id: BAM-to-SAM.
done # install 'bam_to_sam'
Install S-MART dependencies
--
*Bernardo Bello Ortí*
PhD student
CReSA-IRTA
Campus de Bellaterra-Universitat Autònoma de Barcelona
Edifici CReSA
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *
8 years, 9 months
Installing S-Mart on Mac OSX local instance (updated)
by Bernardo Bello
Hi,
I am having problems to install a tool from tool shed named S_MART on my
local Galaxy. In fact, its the first tool I'm trying to install.
The reason to install S-MART is to use DETR'PROK in Galaxy.
Here is the 'error' Galaxy shows after installing some programs from
toolshed.<https://drive.google.com/file/d/0B8-ZAuZe8jldN3ptYzE5N0p2ZGM/edit?usp=sha...>
I've seen this related post, but I don't know if we are talking about the
same problem.<http://dev.list.galaxyproject.org/Problem-installing-tool-Galaxy-local-td...>
Here are the commands aI've used up to now:
Thanks, Bernardo
P.S. Sorry for the duplicated email, I mistyped the subject in the
previous one.
hg clone https://bitbucket.org/galaxy/galaxy-dist/
cd galaxy-dist
hg update stable
sh run.sh # gave errors, so see below
# solve problem at startup (
https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html)
% export LC_ALL='en_US.UTF-8'
% sh run.sh
done # Go to http://localhost:8080/ and register as popnard(a)gmail.com
# Setup admin user (https://wiki.galaxyproject.org/Admin/Interface). To
give a user Galaxy admin privileges, add their Galaxy login ( email ) to
the list in the following config setting in the Galaxy configuration file
universe_wsgi.ini.
admin_users = popnard(a)gmail.com
# Set 'Tool Dependencies'
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show&...
mkdir tool_dependency_dir
done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy
provides a method for managing the dependencies of Galaxy tools installed
from the Tool Shed. In this case, it is simply necessary to set the
tool_dependency_dir option of universe_wsgi.ini to a path writable by the
Galaxy server.
done # restart server
First, I modified the universe_wsgi.ini file by removing the "#" before the
tool_config_file and tool_path lines. #
http://user.list.galaxyproject.org/Installing-new-tools-from-the-tool-she...
# Then, I created a shed_tools folder in my $HOME directory before
modifying the shed_tool_conf.xml file
<?xml version="1.0"?>
<toolbox tool_path="$HOME/shed_tools">
</toolbox>
done # INSTALL R
done # ADD R PACKAGES
R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in%
rownames(installed.packages()) == FALSE){install.packages("RColorBrewer",
repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in%
rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos =
c("http://cran.rstudio.com/"), dependencies = TRUE)}'
--
*Bernardo Bello Ortí*
PhD student
CReSA-IRTA
Campus de Bellaterra-Universitat Autònoma de Barcelona
Edifici CReSA
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *
8 years, 9 months
Data Tables and *.loc files: Using named columns versus from_data_table
by Peter Cock
Hi all,
In discussion about adding an NCBI BLAST data manager
https://github.com/peterjc/galaxy_blast/issues/22 based on
Dan's example, Michael Li has suggested using the new(ish)
Data Table functionality of Galaxy for using *.loc files:
https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
Currently the BLAST+ wrappers access the blastdb.loc file
for picking a system installed nucleotide BLAST database
like this:
<param name="database" type="select" label="Nucleotide BLAST database">
<options from_file="blastdb.loc">
<column name="value" index="0"/>
<column name="name" index="1"/>
<column name="path" index="2"/>
</options>
</param>
See https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus...
With the from_data_table feature this which would be much shorter:
<param name="database" type="select" label="Nucleotide BLAST database">
<options from_data_table="blastdb" />
</param>
For this to work, the column information must instead be
defined centrally in ``tool_data_table_conf.xml`` (via a
``tool_data_table_conf.xml.sample`` file), e.g.
<table name="blastdb" comment_char="#">
<columns>value, name, path</columns>
<file path="tool-data/blastdb.loc" />
</table>
For simple tools this seems quite neat, but within a single tool
suite using XML macros seems equally effective for centrally
defining the columns in the *.loc files (we do this currently).
However, what worries me is the data table XML configuration
file adds a new complexity for dependency management between
different ToolShed repositories using a *.loc file (like the *.loc
files for BLAST databases).
For the BLAST database *.loc files, the simplest solution seems
to be not to use the Data Tables feature (as we do now).
The next best solution seems to be to put the sample *.loc files
and associated data table definition XML files into a shared
ToolShed repository (called called blast_data_tables, or
blast_databases?) which would be declared as a dependency
of anything using the BLAST database *.loc files (e.g. the
BLAST+ wrappers and any data managers).
[This would be like the existing blast_datatypes ToolShed
repository which is a declared dependency of many tools
using BLAST]
Is that a good plan? What benefits does it have over simply
not using the Data Table functionality?
Thanks,
Peter
8 years, 9 months
automatically adding fasta files to "built-in" databases and selecting files questions
by Nikhil Joshi
Hi all,
We have a local install of Galaxy that we use for testing for our
bioinformatics courses. I am creating some new tool interfaces for the
install. I want to create a tool that will allow a user to automatically
add a fasta database to the "built-in" databases (without needing to reboot
the server). Is this possible?
Along with that issue is that the number of databases for this tool can
number in the thousands. Is there a way to easily search the built-in
databases for the database you are looking for, and then use that database
in a tool? Right now, it is an enormous drop down list which is really
annoying and unwieldy.
Finally, these tools can take multiple input files, but I really don't like
the way galaxy handles that where you have to continually click on "Add
another file". Is there a method or work-around in galaxy where you can
have a multi-file select?
- Nik.
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
8 years, 9 months
visualization button
by Philippe Moncuquet
Hi,
I have developed a simple script that give some statistics on an assemble.
It generates a tabular output. The visualization button is not available
when I extend the output in the history pane. Is there any code that I need
to put in my xml wrapper to get this button available ?
Regards,
Philip
8 years, 9 months
