Re: [galaxy-dev] nglims/services/python
Thanks Ross! Unfortunately I still have the same error. Although I can
directly run galaxy via the command run.sh, the system service fails with
the error I showed before. In other words this works as the galaxy user:
./run.sh --restart
This does not work when I run it as root (or when root runs it as the
machine starts up):
service chapman-galaxy start
This is the init file which I slightly modified from the contrib directory
(which now resides under /etc/init.d/). There must be some fundamental
reason why running it as root does not work that I don't understand. I
actually don't think it's this init script that is the problem because a
vanilla install of Galaxy works fine using system galaxy start and when
it is under init.d.
#!/bin/bash
# Author: James Casbon, 2009
# Modified by Lee Katz 2013 for this specific system
### BEGIN INIT INFO
# Provides: chapman-galaxy
# Required-Start: $network $local_fs $mysql
# Required-Stop:
# Default-Start:2 3 4 5
# Default-Stop: 0 1 6
# Short-Description:Chapman-Galaxy
### END INIT INFO
. /lib/lsb/init-functions
USER=galaxy
GROUP=galaxy
DIR=/home/galaxy/bin/chapman-dist
PYTHON=/usr/bin/python
OPTS=-ES ./scripts/paster.py serve --log-file $DIR/galaxy.log
universe_wsgi.ini
PIDFILE=/var/run/galaxy-chapman.pid
case ${1:-''} in
'start')
log_daemon_msg Starting Chapman-Galaxy
if start-stop-daemon --chuid $USER --group $GROUP --start
--make-pidfile \
--pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON --
$OPTS; then
log_end_msg 0
else
log_end_msg 1
fi
;;
'stop')
log_daemon_msg Stopping Chapman-Galaxy
if start-stop-daemon --stop --pidfile $PIDFILE; then
log_end_msg 0
else
log_end_msg 1
fi
;;
'restart')
# restart commands here
$0 stop
$0 start
;;
'status')
if [ -f $PIDFILE ]; then
pid=`cat $PIDFILE`;
log_daemon_msg Chapman-galaxy pid is $pid
else
log_daemon_msg Chapman-galaxy does not have a pid
fi
;;
*) # no parameter specified
echo Usage: $SELF start|stop|restart|reload|force-reload|status
exit 1
;;
esac
On Sat, Jun 15, 2013 at 12:38 AM, Ross ross.laza...@gmail.com wrote:
My mistake - try
(sudo) pip install pyaml
That's what the pip yaml repo is called...
On Sat, Jun 15, 2013 at 11:38 AM, Ross ross.laza...@gmail.com wrote:
Hi, Lee - the last line of that error dump might be worth thinking about.
It seems clear enough. Your python interpreter seems unable to import a
module called yaml
Perhaps you need to (eg) do
pip install yaml
in the virtualenv (or sudo ... for the system one if not using a
virtualenv) you're running your Galaxies with?
I hope this helps.
On Fri, Jun 14, 2013 at 11:52 PM, Lee Katz lsk...@gmail.com wrote:
Hi, I am running into an error that I bet has a simple solution. I would
appreciate any help. Thanks.
I am running Brad Chapman's LIMS extension locally on Ubuntu 12. I also
installed it as a service under /etc/init.d/chapman-galaxy using
contrib/galaxy.debian-init . It works when I run it directly (./run.sh
--reload)
When I run a version of Galaxy without nglims as a service, there is no
error.
When I run a version of Galaxy with nglims, not as a service (run.sh),
there is no error.
However, when I run the same version of Galaxy with nglims as a service,
there is an error. I don't understand well enough what the difference is
when I run it as a service to diagnose this problem. The lines leading to
the error from the log file is below. Something to do with yaml not being
loaded, but I know I installed python-yaml through aptitude.
galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,873 Enabling
'requests' controller, class: Requests
galaxy.webapps.galaxy.controllers library_common
galaxy.webapps.galaxy.controllers.library_common
galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,874 Enabling
'library_common' controller, class: LibraryCommon
galaxy.webapps.galaxy.controllers nglims
galaxy.webapps.galaxy.controllers.nglims
Traceback (most recent call last):
File ./scripts/paster.py, line 34, in module
command.run()
File
/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 84, in run
invoke(command, command_name, options, args[1:])
File
/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 123, in invoke
exit_code = runner.run(args)
File
/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 218, in run
result = self.command()
File
/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py,
line 276, in command
relative_to=base, global_conf=vars)
File
/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py,
line 313, in loadapp
**kw)
[galaxy-dev] trimest tool cuts the begining of my seq names in the output fasta file
Dear galaxy developers, When I use the EMBOSS tool: trimesthttps://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS%3A%20trimest102/5.0.0, Trim poly-A tails off EST sequences , within galaxy The sequences names in the fasta output file comes out without their beginning, for instance: gi|259479195|dbj|AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds Will be shortened into: AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds How can I keep the beginning of the sequence names? Am I doing something wrong? Many thanks for your help Inbar [Description: logo_50prcnt] Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Building 51, room 323 Email: inba...@bgu.ac.ilmailto:inba...@bgu.ac.il Tel: +972-8-6428676 Fax: +972-8-6479035 Web: http://bioinfo.bgu.ac.ilhttp://bioinfo.bgu.ac.il/ inline: image001.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] bowtie2 on galaxy cloudman?
Is bowtie2 available on galaxy cloudman? If not, when will it be available? Thanks, Theresa Murphy The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] dynamically load and run R scripts
Hi guys, I was searching for a possiblity to dynamically load and run R scripts and I found http://dev.list.galaxyproject.org/dynamic-loading-of-tools-tt4138600.html I know that it might be a security issue, but we only have a local instance here. Optimally an R script can be loaded into the history. Subsequently, this script can be execute via tool that takes this script and some parameters and returns the result. Is anything like that out there? Could anyone give me a reference? Thanks a lot, Jens ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] nglims/services/python
I figured it out after some more digging. The /etc/init.d script had a
Python flag -S which narrows down the paths where Python will search for
modules. The path with pyaml was excluded and could not be found. So, I
removed the -S flag.
And then, I almost forgot to run the command to make it start up with the
reboot and so I will put it here for anyone who might find this post helpful
update-rc.d chapman-galaxy defaults
On Mon, Jun 17, 2013 at 9:24 AM, Lee Katz lsk...@gmail.com wrote:
Thanks Ross! Unfortunately I still have the same error. Although I can
directly run galaxy via the command run.sh, the system service fails with
the error I showed before. In other words this works as the galaxy user:
./run.sh --restart
This does not work when I run it as root (or when root runs it as the
machine starts up):
service chapman-galaxy start
This is the init file which I slightly modified from the contrib directory
(which now resides under /etc/init.d/). There must be some fundamental
reason why running it as root does not work that I don't understand. I
actually don't think it's this init script that is the problem because a
vanilla install of Galaxy works fine using system galaxy start and when
it is under init.d.
#!/bin/bash
# Author: James Casbon, 2009
# Modified by Lee Katz 2013 for this specific system
### BEGIN INIT INFO
# Provides: chapman-galaxy
# Required-Start: $network $local_fs $mysql
# Required-Stop:
# Default-Start:2 3 4 5
# Default-Stop: 0 1 6
# Short-Description:Chapman-Galaxy
### END INIT INFO
. /lib/lsb/init-functions
USER=galaxy
GROUP=galaxy
DIR=/home/galaxy/bin/chapman-dist
PYTHON=/usr/bin/python
OPTS=-ES ./scripts/paster.py serve --log-file $DIR/galaxy.log
universe_wsgi.ini
PIDFILE=/var/run/galaxy-chapman.pid
case ${1:-''} in
'start')
log_daemon_msg Starting Chapman-Galaxy
if start-stop-daemon --chuid $USER --group $GROUP --start
--make-pidfile \
--pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON --
$OPTS; then
log_end_msg 0
else
log_end_msg 1
fi
;;
'stop')
log_daemon_msg Stopping Chapman-Galaxy
if start-stop-daemon --stop --pidfile $PIDFILE; then
log_end_msg 0
else
log_end_msg 1
fi
;;
'restart')
# restart commands here
$0 stop
$0 start
;;
'status')
if [ -f $PIDFILE ]; then
pid=`cat $PIDFILE`;
log_daemon_msg Chapman-galaxy pid is $pid
else
log_daemon_msg Chapman-galaxy does not have a pid
fi
;;
*) # no parameter specified
echo Usage: $SELF start|stop|restart|reload|force-reload|status
exit 1
;;
esac
On Sat, Jun 15, 2013 at 12:38 AM, Ross ross.laza...@gmail.com wrote:
My mistake - try
(sudo) pip install pyaml
That's what the pip yaml repo is called...
On Sat, Jun 15, 2013 at 11:38 AM, Ross ross.laza...@gmail.com wrote:
Hi, Lee - the last line of that error dump might be worth thinking
about.
It seems clear enough. Your python interpreter seems unable to import a
module called yaml
Perhaps you need to (eg) do
pip install yaml
in the virtualenv (or sudo ... for the system one if not using a
virtualenv) you're running your Galaxies with?
I hope this helps.
On Fri, Jun 14, 2013 at 11:52 PM, Lee Katz lsk...@gmail.com wrote:
Hi, I am running into an error that I bet has a simple solution. I
would appreciate any help. Thanks.
I am running Brad Chapman's LIMS extension locally on Ubuntu 12. I
also installed it as a service under /etc/init.d/chapman-galaxy using
contrib/galaxy.debian-init . It works when I run it directly (./run.sh
--reload)
When I run a version of Galaxy without nglims as a service, there is no
error.
When I run a version of Galaxy with nglims, not as a service (run.sh),
there is no error.
However, when I run the same version of Galaxy with nglims as a
service, there is an error. I don't understand well enough what the
difference is when I run it as a service to diagnose this problem. The
lines leading to the error from the log file is below. Something to do
with yaml not being loaded, but I know I installed python-yaml through
aptitude.
galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,873 Enabling
'requests' controller, class: Requests
galaxy.webapps.galaxy.controllers library_common
galaxy.webapps.galaxy.controllers.library_common
galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,874 Enabling
'library_common' controller, class: LibraryCommon
galaxy.webapps.galaxy.controllers nglims
galaxy.webapps.galaxy.controllers.nglims
Traceback (most recent call last):
File ./scripts/paster.py, line 34, in module
command.run()
File
/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 84, in run
invoke(command, command_name, options, args[1:])
File
Re: [galaxy-dev] Cloudman - Can you label volumes after user specifies the volume size they want?
Yes, this is good suggestion. The good news is that the functionality is already implemented in the soon-to-be-released version of CloudMan. On Fri, Jun 14, 2013 at 6:52 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: Initially only one volume is shown on Amazon's EC2 management console. Then, after the user goes into the instance's URL and logs into Cloudman, they are prompted with a box called Initial cluster configuration where they specify the size of the volume they want. THEN, three nameless volumes are produced. The problem here is that the volumes are nameless, and this makes cleanup on Amazon's EC2 console difficult since we have no way of knowing these volumes are related to the Galaxy cloudman AMI. I am wondering if there is a way to pass a script to Cloudman that it will run once the volumes are created (ie. After the user goes to the URL and specifies the volume size they want). The script will be used to add name= tags for each of the three additional volumes. Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] bowtie2 on galaxy cloudman?
Hi Teresa, It's not available on the curent release but we are finalizing a new release that will make addition of tools very straightforward so, if not included by default, it will be easy to do. Thanks for using Galaxy. On Sun, Jun 16, 2013 at 4:25 PM, Murphy, Theresa tmur...@pathology.wustl.edu wrote: Is bowtie2 available on galaxy cloudman? If not, when will it be available? Thanks, Theresa Murphy The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cloudman - can you specify the volume size without needing to access the instance URL?
It is quite tedious to do so if you have many instances running. Is there a way to automate this step? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cloudman - can you specify the volume size without needing to access the instance URL?
If you're starting a bunch of new clusters at once, I'd look into using the Share-an-instance functionality to create a single base configuration with the volume size you prefer. This would allow you to have a predefined volume (with a specific size) that starts automatically. The share_string can be specified in userData and would automatically initialize the new cluster to whatever saved state you snapshot. Dannon On Mon, Jun 17, 2013 at 11:57 AM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: It is quite tedious to do so if you have many instances running. Is there a way to automate this step? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] The requested URL /cgi-bin-root/hgTracks was not found on this server
Hi, I starting getting this error since late galaxy update I get data from UCSC Main (local), but when I click display at UCSC main I get: Not Found The requested URL /cgi-bin-root/hgTracks was not found on this server. Please help Thanks --R ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Startup error, Galaxy DB got corrupted?
Dear list,
Yesterday, I noticed that the user quota setting on our Galaxy had a
problem - the list of user email address is missing from the manage quota
page. So I thought to give a Galaxy codebase update a try after backing up
the Galaxy dir and the database.
Running hg head gives me:
==
postgres@ubuntu:/mnt/galaxyTools/galaxy-2013-05-13$ hg head
changeset: 10003:b4a373d86c51
tag: tip
parent: 10001:471484ff8be6
user:greg
date:Wed Jun 12 11:48:09 2013 -0400
summary: Add targets to Repository Actions menu items.
==
I updated the DB schema to support the code update. But the restart of
Galaxy failed with an error in paster.log:
==
Traceback (most recent call last):
File
/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/webapps/galaxy/buildapp.py,
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/app.py, line 164, in
__init__
self.job_manager = manager.JobManager( self )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/manager.py,
line 36, in __init__
self.job_handler.start()
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 34, in start
self.job_queue.start()
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 77, in start
self.__check_jobs_at_startup()
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 125, in __check_jobs_at_startup
self.dispatcher.recover( job, job_wrapper )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 620, in recover
self.job_runners[runner_name].recover( job, job_wrapper )
File
/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/runners/local.py, line
128, in recover
job_wrapper.change_state( model.Job.states.ERROR, info = This job was
killed when Galaxy was restarted. Please retry the job. )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/__init__.py,
line 824, in change_state
dataset.state = state
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/model/__init__.py,
line 1163, in set_dataset_state
object_session( self ).flush() #flush here, because hda.flush() won't
flush the Dataset object
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1718, in flush
self._flush(objects)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1789, in _flush
flush_context.execute()
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 331, in execute
rec.execute(self)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 475, in execute
uow
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 59, in save_obj
mapper, table, update)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 485, in _emit_update_statements
execute(statement, params)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1449, in execute
params)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1698, in _execute_context
context)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1691, in _execute_context
context)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py,
line 331, in do_execute
cursor.execute(statement, parameters)
InternalError: (InternalError) could not read block 326 in file
base/257536/259291: read only 0 of 8192 bytes
'UPDATE dataset SET update_time=%(update_time)s, state=%(state)s WHERE
dataset.id = %(dataset_id)s' {'update_time': datetime.datetime(2013, 6, 17,
12, 42, 38, 145908), 'state': 'error', 'dataset_id': 68792}
==
I went on to check the Galaxy database (in postgres) which confirmed the
error in the paster.log.
==
galaxy=# select * from dataset where id =
68792;
id |create_time |update_time | state |
deleted | purged | purgable | external_filename | _extra_files_path |
file_size | total_size | object_store_id | uuid
---+++---+-++--+---+---+---++-+--
68792 | 2013-06-12
Re: [galaxy-dev] dynamically load and run R scripts
Hi Jens, the toolfactory (install from the admin menu - it's in the main toolshed) allows admin users to paste and run arbitrary R scripts. Yes, there are serious security issues exposing unrestricted scripting! So the toolfactory only works for admin users and should never be installed on public/production instance but you can generate a new Galaxy tool from your script once it runs correctly, in a toolshed compatible format. Once installed from a toolshed, the generated tools are ordinary Galaxy tools with normal Galaxy security. For gory details see https://bitbucket.org/fubar/galaxytoolfactory On Mon, Jun 17, 2013 at 11:32 PM, Keilwagen, Jens jens.keilwa...@jki.bund.de wrote: Hi guys, I was searching for a possiblity to dynamically load and run R scripts and I found http://dev.list.galaxyproject.org/dynamic-loading-of-tools-tt4138600.html I know that it might be a security issue, but we only have a local instance here. Optimally an R script can be loaded into the history. Subsequently, this script can be execute via tool that takes this script and some parameters and returns the result. Is anything like that out there? Could anyone give me a reference? Thanks a lot, Jens ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cannot configure DRMAA
Hello. I have installed Galaxy and run it successfully. Now I am trying to
configure it to use DRMAA job runner. I created a job_conf.xml file as
explained in the Galaxy wiki:
?xml version=1.0?
job_conf
plugins
plugin id=sge type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=4/
/plugins
destinations default=sge_default
destination id=sge_default runner=drmaa/
/destinations
/job_conf
The galaxy user has the necessary environment variable:
$ echo $DRMAA_LIBRARY_PATH
/opt/sge/lib/lx-amd64/libdrmaa.so
But then Galaxy does not start. Here are the final log messages:
galaxy.jobs DEBUG 2013-06-17 17:32:27,715 Loading job configuration from
./job_conf.xml
Traceback (most recent call last):
File
/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/app.py, line 97, in
__init__
self.job_config = jobs.JobConfiguration(self)
File /mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py,
line 109, in __init__
self.__parse_job_conf_xml(tree)
File /mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py,
line 159, in __parse_job_conf_xml
self.default_handler_id = self.__get_default(handlers, self.handlers.keys())
File /mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py,
line 288, in __get_default
rval = parent.get('default')
AttributeError: 'NoneType' object has no attribute 'get'
Removing PID file galaxy-web1.pid
I am using the following to start Galaxy:
/bin/sh run.sh --pid-file galaxy.pid --log-file galaxy.log
I have updated my Galaxy install to the latest stable version, but the problem
persists. Any help will be much appreciated. Please note that Galaxy runs ok
without the job_conf.xml file. Is there some configuration I am missing? Thanks.
Viren
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[galaxy-dev] invalid frame access with data source
When loading a data source in an iframe, the galaxy js is doing some sort
of invalid probing of the frame, leading to this error:
Blocked a frame with origin http://pk:8080; from accessing a frame with
origin https://tcga1.kilokluster.ucsc.edu;.
pk:8080 is the galaxy frame. Here is the offending code:
jQuery( function() {
$(iframe#galaxy_main).load( function() {
$(this).contents().find(form).each( function() {
What is this? And is there some way to work around it?
On chrome it doesn't appear to cause any problem, however on FF it causes
the js to abort in both frames, preventing the data source callback.
b.c.
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Re: [galaxy-dev] Startup error, Galaxy DB got corrupted?
The error ERROR: could not read block 326 in file base/257536/259291:
read only 0 of 8192 bytes line makes me wonder if your database may have
been corrupt prior to the upgrade/dump. Some brief googling suggests that
this could be hardware failure induced among other things. Can you check
the postgres logs for any likely explanations?
How exactly did you perform your database backup and attempted recreation?
-Dannon
On Mon, Jun 17, 2013 at 5:12 PM, Leon Mei hailiang@nbic.nl wrote:
Dear list,
Yesterday, I noticed that the user quota setting on our Galaxy had a
problem - the list of user email address is missing from the manage quota
page. So I thought to give a Galaxy codebase update a try after backing up
the Galaxy dir and the database.
Running hg head gives me:
==
postgres@ubuntu:/mnt/galaxyTools/galaxy-2013-05-13$ hg head
changeset: 10003:b4a373d86c51
tag: tip
parent: 10001:471484ff8be6
user:greg
date:Wed Jun 12 11:48:09 2013 -0400
summary: Add targets to Repository Actions menu items.
==
I updated the DB schema to support the code update. But the restart of
Galaxy failed with an error in paster.log:
==
Traceback (most recent call last):
File
/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/webapps/galaxy/buildapp.py,
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/app.py, line 164,
in __init__
self.job_manager = manager.JobManager( self )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/manager.py,
line 36, in __init__
self.job_handler.start()
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 34, in start
self.job_queue.start()
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 77, in start
self.__check_jobs_at_startup()
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 125, in __check_jobs_at_startup
self.dispatcher.recover( job, job_wrapper )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/handler.py,
line 620, in recover
self.job_runners[runner_name].recover( job, job_wrapper )
File
/mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/runners/local.py, line
128, in recover
job_wrapper.change_state( model.Job.states.ERROR, info = This job was
killed when Galaxy was restarted. Please retry the job. )
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/jobs/__init__.py,
line 824, in change_state
dataset.state = state
File /mnt/galaxyTools/galaxy-2013-05-13/lib/galaxy/model/__init__.py,
line 1163, in set_dataset_state
object_session( self ).flush() #flush here, because hda.flush() won't
flush the Dataset object
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1718, in flush
self._flush(objects)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py,
line 1789, in _flush
flush_context.execute()
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 331, in execute
rec.execute(self)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py,
line 475, in execute
uow
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 59, in save_obj
mapper, table, update)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py,
line 485, in _emit_update_statements
execute(statement, params)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1449, in execute
params)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1698, in _execute_context
context)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py,
line 1691, in _execute_context
context)
File
/mnt/galaxyTools/galaxy-2013-05-13/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py,
line 331, in do_execute
cursor.execute(statement, parameters)
InternalError: (InternalError) could not read block 326 in file
base/257536/259291: read only 0 of 8192 bytes
'UPDATE dataset SET update_time=%(update_time)s, state=%(state)s WHERE
dataset.id = %(dataset_id)s' {'update_time': datetime.datetime(2013, 6,
17, 12, 42, 38, 145908), 'state':
