Re: [galaxy-dev] Galaxy Server on Bio-Linux
On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote: Dear Galaxy Developers, We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford. We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe! Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy). We will be happy to hear any comments regarding these efforts and we hope that this will be a useful resource for all Galaxy users. Once the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource. Best wishes, Tim, Soon and Mesude Hi Mesude, This is fantastic, thanks for letting us know, and please do post up if there is anything we can help with. Also, if you're not aware, Galaxy's cloud offering is built on CloudBioLinux, which itself is built on Bio-Linux. --nate -- Dr. Mesude Bicak mbi...@ceh.ac.uk Bioinformatician Bio-Linux Developer NERC Biomolecular Analysis Facility (NBAF) http://nbaf.nerc.ac.uk NERC Environmental Bioinformatics Centre (NEBC) http://nebc.nerc.ac.uk Molecular Evolution and Bioinformatics Group Centre for Ecology and Hydrology http://ceh.ac.uk Maclean Building, Benson Lane Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB Office Tel: +44 1491 69 2705-- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. ___ 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/ ___ 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/
Re: [galaxy-dev] Stuck at Job is waiting to run when using Get data
On Dec 22, 2011, at 11:13 AM, Liang Zhang wrote: Dear Galaxy team: I was trying to use the Get Data – Upload File tool yesterday. I uploaded all files through FTP. Then selected them in “Files uploaded via FTP”, selected “auto-detect” + ”Mouse July 2007 (NCBI37/mm9) (mm9)” and clicked execute. My jobs are registered, but they all stuck at “Job is waiting to run”. I waited for over 16 hours and they are still showing “Job is waiting to run”. I tried to click “Run the job again” and it says “Could not find the job for this dataset”. I tried to delete all the jobs, log out and log in. Then add jobs again, but still no luck, they all still stuck at “Job is waiting to run”. My data files are 8 x 3Gb sized fastq files. Please help. Liangz Hi, Due to extremely high load at the time, jobs were delayed. This has been resolved, so please let us know if you have any further problems with running jobs. Sorry for the inconvenience and thanks for using Galaxy. Thanks, --nate ___ 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/ ___ 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/
[galaxy-dev] proxy server settings (or documentation amendment)
I set up my Apache server to act as a proxy server based on the docs at http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy My pages aren't loading correctly and I discovered that since I have galaxy installed as its own user, the apache user account does not have access to the galaxy files. I need to change the permissions of the galaxy files to make them available to the apache user. Someone may want to update the docs to reflect that this change needs to be made... ___ 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/
Re: [galaxy-dev] manage_db.sh upgrade fails after fresh install of Galaxy
Your database is not cleanly dropped when you start up your Galaxy server -
notice all of the migration scripts that fail because table columns, etc
already exist. Here's an example:
0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
request_type table failed: (ProgrammingError) column deleted of relation
request_type already exists
On Jan 3, 2012, at 11:59 AM, Iry Witham wrote:
Hi Nate,
I do not create any tables manually. I simply create the database and
setup users and roles. I do the following:
initdb D /local/postgresql/data
pg_ctl D /local/postgresql/data I /local/postgresql/pgsql.log start
createdb galaxy_1
Sudo su - postgres
pgsql galaxy_1
CREATE USER galaxy
CREATE USER galaxyftp
ALTER ROLE galaxyftp PASSWORD 'dbpassword'
GRANT SELECT ON galaxy_user TO galaxyftp (Note: this fails prior to
launching galaxy server for the first time)
I start galaxy and run 'sh manage_db.sh upgrade'.
0 - 1...
done
1 - 2...
done
2 - 3...
done
3 - 4...
done
4 - 5...
done
5 - 6...
This migration script changes certain values in the
history_dataset_association.extension
column, specifically 'qual' is chaged to be 'qual454'.
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_
r6498-py2.6.egg/sqlalchemy/sql/compiler.py:336: SAWarning: The SQLAlchemy
psycopg2 dialect now automatically escapes '%' in text() expressions to
'%%'.
BIND_PARAMS.sub(do_bindparam, self.post_process_text(textclause.text))
done
6 - 7...
This migration script creates the new history_user_share_association
table, and adds
a new boolean type column to the history table. This provides support for
sharing
histories in the same way that workflows are shared.
done
7 - 8...
This migration script adds the following new tables for supporting Galaxy
forms:
1) form_definition_current
2) form_definition
3) form_values
4) request_type
5) request
6) sample
7) sample_state
8) sample_event
done
8 - 9...
This migration script adds a new column to 2 tables:
1) a new boolean type column named 'submitted' to the 'request' table
2) a new string type column named 'bar_code' to the 'sample' table
done
9 - 10...
This migration script adds the
history_dataset_association_display_at_authorization table, which
allows 'private' datasets to be displayed at external sites without making
them public.
If using mysql, this script will display the following error, which is
corrected in the next migration
script: history_dataset_association_display_at_authorization table failed:
(OperationalError)
(1059, 'Identifier name
'ix_history_dataset_association_display_at_authorization_update_time'
is too long.
done
10 - 11...
This script fixes a problem introduced in the previous migration script (
9-10 ). MySQL
has a name length limit and thus the index
'ix_hdadaa_history_dataset_association_id' has
to be manually created.
done
11 - 12...
This script adds a new user_address table that is currently only used with
sample requests, where
a user can select from a list of his addresses to associate with the
request. This script also
drops the request.submitted column which was boolean and replaces it with
a request.state column
which is a string, allowing for more flexibility with request states.
0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
request_type table failed: (ProgrammingError) column deleted of relation
request_type already exists
'\nALTER TABLE request_type ADD deleted BOOLEAN' {}
0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
request_type table failed: (ProgrammingError) column deleted of relation
request_type already exists
'\nALTER TABLE request_type ADD deleted BOOLEAN' {}
done
12 - 13...
This migration script eliminates all of the tables that were used for the
1st version of the
library templates where template fields and contents were each stored as a
separate table row
in various library item tables. All of these tables are dropped in this
script, eliminating all
existing template data. A total of 14 existing tables are dropped.
We're now basing library templates on Galaxy forms, so field contents are
stored as a jsonified
list in the form_values table. This script introduces the following 3 new
Re: [galaxy-dev] [galaxy-user] (OperationalError) unable to open database file
On Dec 29, 2011, at 12:15 AM, Cai Shaojiang wrote: Dear friends, We are trying to install galaxy on the server (ubuntu 11), just by following the steps on the page Get Galaxy: Galaxy Download and Installation of galaxy wiki. But when we start running it, it shows the following error message. OperationalError: (OperationalError) unable to open database file u'INSERT INTO galaxy_session (create_time, update_time, user_id, remote_host, remote_addr, referer, current_history_id, session_key, is_valid, prev_session_id, disk_usage) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)' ['2011-12-29 04:52:46.575702', '2011-12-29 04:52:46.575719', None, '10.50.70.45', '10.50.70.45', None, None, '5a38b2a7e6d77a7145726cb0881eadf6', 1, None, None] It seems something wrong with the write permission. Could you give any hint where the problem could be? Thanks. Hi Cai, I've moved this over to the galaxy-dev list since it pertains to a local installation. Please make sure that the galaxy-dist/database/ directory is writable by the user running the Galaxy server. Also, if you plan to use this server for anything other than single-user development, I would suggest switching to a PostgreSQL server. This is trivial on Ubuntu (apt-get install postgresql, createuser/createdb, then edit universe_wsgi.ini as described at http://usegalaxy.org/production ). --ndate Best regards. Yours: Cai ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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/
Re: [galaxy-dev] Torque / scrambling pbs_python
On Dec 29, 2011, at 4:29 PM, Ryan Golhar wrote:
Hi - I've just finished installing a ROCKS 5.4.3 cluster and am now adding
Galaxy to it. We are using torque instead of SGE. I see the Wiki docs at
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster state I need to
scramble pbs_python by doing:
LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python
I have libtorque installed in /usr/lib64:
[galaxy@bic x86_64]$ ll /usr/lib64/libtorque.*
-rw-r--r-- 1 root root 536862 Dec 28 12:32 /usr/lib64/libtorque.a
-rwxr-xr-x 1 root root810 Dec 28 12:32 /usr/lib64/libtorque.la
lrwxrwxrwx 1 root root 18 Dec 28 13:50 /usr/lib64/libtorque.so -
libtorque.so.2.0.0
lrwxrwxrwx 1 root root 14 Dec 28 13:50 /usr/lib64/libtorque.so.0 -
libtorque.so.2
lrwxrwxrwx 1 root root 18 Dec 28 13:50 /usr/lib64/libtorque.so.2 -
libtorque.so.2.0.0
-rwxr-xr-x 1 root root 766431 Dec 28 12:32 /usr/lib64/libtorque.so.2.0.0
So I then run (and get the error shown at the bottom):
[galaxy@bic x86_64]$ cd
[galaxy@bic ~]$ cd galaxy-dist/
[galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64/libtorque.so.2.0.0 python
scripts/scramble.py -e pbs_python
Hi Ryan,
$LIBTORQUE_DIR should be the path to the directory containing libtorque, so try:
[galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64 python scripts/scramble.py
-e pbs_python
Although it looks like the build (below) succeeded anyway since libtorque.so is
in a system lib directory.
fetch_one(): Trying to fetch:
http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz
fetch_one(): Fetched to:
/home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz
unpack_source(): Unpacked to:
/home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python
copy_build_script(): Using build script
/home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in
/home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python:
/share/apps/Python-2.6.7/bin/python scramble.py
---
This script requires setuptools version 0.6c11 to run (even to display
help). I will attempt to download it for you (from
http://pypi.python.org/packages/2.6/s/setuptools/), but
you may need to enable firewall access for this script first.
I will start the download in 8 seconds.
(Note: if this machine does not have network access, please obtain the file
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg
and place it in this directory before rerunning this script.)
---
Downloading
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg
checking for pbs-config... /usr/bin/pbs-config
Found torque version: 2.5.9
checking for python... /share/apps/Python-2.6.7/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.6/site-packages
checking for python extension module directory...
${exec_prefix}/lib/python2.6/site-packages
configure: creating ./config.status
config.status: creating Makefile
config.status: creating setup.py
scramble(): Patching setup.py
running egg_info
creating src/pbs_python.egg-info
writing src/pbs_python.egg-info/PKG-INFO
writing top-level names to src/pbs_python.egg-info/top_level.txt
writing dependency_links to src/pbs_python.egg-info/dependency_links.txt
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
reading manifest file 'src/pbs_python.egg-info/SOURCES.txt'
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.6
copying src/pbs.py - build/lib.linux-x86_64-2.6
copying src/PBSQuery.py - build/lib.linux-x86_64-2.6
running build_ext
building '_pbs' extension
creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DTORQUE_2_4
-I/share/apps/Python-2.6.7/include/python2.6 -c src/pbs_wrap.c -o
build/temp.linux-x86_64-2.6/src/pbs_wrap.o
src/pbs_wrap.c:2622: warning: function declaration isn't a prototype
src/pbs_wrap.c:2630: warning: function declaration isn't a prototype
gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o -L/usr/lib64
-ltorque -o build/lib.linux-x86_64-2.6/_pbs.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/pbs.py - build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/PBSQuery.py - build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/_pbs.so -
[galaxy-dev] load balancing with Apache
Hi all - I'm setting up Galaxy under Apache and following the guide for a
production environment. I've got the proxy server running properly and am
now setting up load balancing. I currently start galaxy (for testing)
using 'sh run.sh --reload' so I can stop galaxy using Ctrl-C.
I'm following the instructions on
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
There is a mistake in the run.sh script provided for Starting and Stopping
the web app and runner services. The script right now shows:
cd `dirname $0`
for i in {0..1}; do
python ./scripts/paster.py serve universe_wsgi.webapp.ini
--server-name=web$i --pid-file=web$i.pid --log-file=web$i.log $@
done
python ./scripts/paster.py serve universe_wsgi.runner.ini
--server-name=runner0 --pid-file=runner0.pid --log-file=runner0.log $@
The problem with this is the python processes don't get backgrounded. So
when this is run, the first web0 python process is invoked, but that's it.
The rest doesn't get run. You need to stop the process with Ctrl-C, but
then only the next web1 process gets started. Ctrl-C then stops web1, then
runner0 gets started.
I changed the script to be:
cd `dirname $0`
for i in {0..1}; do
python ./scripts/paster.py serve universe_wsgi.webapp.ini
--server-name=web$i --pid-file=web$i.pid --log-file=web$i.log --daemon $@
done
python ./scripts/paster.py serve universe_wsgi.runner.ini
--server-name=runner0 --pid-file=runner0.pid --log-file=runner0.log
--daemon $@
I added '--daemon'. The only hiccup to this is after doing this, Ctrl-C is
no longer an option to stop galaxy. So I discovered using 'sh run.sh
--reload' is no longer correct. Instead 'sh run.sh --daemon' and 'sh
run.sh --stop-daemon' should be used. This may want to be included in the
wiki docs.
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Re: [galaxy-dev] load balancing with Apache
On Jan 3, 2012, at 1:19 PM, Ryan wrote:
Hi all - I'm setting up Galaxy under Apache and following the guide for a
production environment. I've got the proxy server running properly and am
now setting up load balancing. I currently start galaxy (for testing) using
'sh run.sh --reload' so I can stop galaxy using Ctrl-C.
I'm following the instructions on
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
There is a mistake in the run.sh script provided for Starting and Stopping
the web app and runner services. The script right now shows:
cd `dirname $0`
for i in {0..1}; do
python ./scripts/paster.py serve universe_wsgi.webapp.ini
--server-name=web$i --pid-file=web$i.pid --log-file=web$i.log $@
done
python ./scripts/paster.py serve universe_wsgi.runner.ini
--server-name=runner0 --pid-file=runner0.pid --log-file=runner0.log $@
The problem with this is the python processes don't get backgrounded. So
when this is run, the first web0 python process is invoked, but that's it.
The rest doesn't get run. You need to stop the process with Ctrl-C, but then
only the next web1 process gets started. Ctrl-C then stops web1, then
runner0 gets started.
I changed the script to be:
cd `dirname $0`
for i in {0..1}; do
python ./scripts/paster.py serve universe_wsgi.webapp.ini
--server-name=web$i --pid-file=web$i.pid --log-file=web$i.log --daemon $@
done
python ./scripts/paster.py serve universe_wsgi.runner.ini
--server-name=runner0 --pid-file=runner0.pid --log-file=runner0.log --daemon
$@
I added '--daemon'. The only hiccup to this is after doing this, Ctrl-C is no
longer an option to stop galaxy. So I discovered using 'sh run.sh --reload'
is no longer correct. Instead 'sh run.sh --daemon' and 'sh run.sh
--stop-daemon' should be used. This may want to be included in the wiki docs.
Hi Ryan,
Thanks for catching this, I've updated the documentation.
--nate
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Re: [galaxy-dev] Quota will not decrease with permanent delete
On Dec 6, 2011, at 2:16 PM, Mary Anne Alliegro wrote: No, it is still reads over 120GB yet the usage is only 26% Hi Mary Anne, Sorry I didn't get back to you sooner. Your usage is currently ~75GB. The difference before may have been due to some other data in your account which was not permanently deleted. If you still find that your disk usage isn't reflecting your actual history sizes, please have a look at this page for details on how to view deleted data: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets And let us know if this doesn't answer any remaining questions. Thanks for using Galaxy, --nate Mary Anne Alliegro Marine Biological Laboratory JOSEPHINE BAY PAUL CENTER FOR COMPARATIVE MOLECULAR BIOLOGY AND EVOLUTION 7 MBL Street Woods Hole, MA 02543 maallie...@mbl.edu 508-289-7419 From: Nate Coraor n...@bx.psu.edu To: Mary Anne Alliegro maallie...@mbl.edu Cc: galaxy-...@bx.psu.edu Sent: Tuesday, December 6, 2011 1:14:32 PM Subject: Re: [galaxy-dev] Quota will not decrease with permanent delete On Nov 30, 2011, at 2:24 PM, Mary Anne Alliegro wrote: Hi Galaxy Users, I have permanently deleted numerous files. My usage % has decreased, but this is NOT reflected in my Gb report (upper right)- it remains the same. Am I missing some phantom trash bin? If not, will Galaxy recalculate my Gb usage so that I may proceed with my project? Thank you, Mary Anne Hi Mary Anne, I believe your usage total is now correct, but if this is not the case, please let us know. Thanks, --nate pastedGraphic.pdf ___ 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/ ___ 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/
Re: [galaxy-dev] how to disable error detection
On Dec 10, 2011, at 8:47 AM, Xuebing Wu wrote: Hi, I'm wondering if there is a way to disable the error detection (output showing red). I was adding some tools to a local Galaxy server. Some of the tool's stdout were directed to a file. The tool ran without an error, but Galaxy treated this standard output as error. Hi Xuebing, Sorry for the delay in response. Please see the following page: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr --nate best, Xuebing ___ 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/ ___ 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/
Re: [galaxy-dev] file upload issue
On Dec 15, 2011, at 4:05 PM, weihong yan wrote: I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of Dataset is uploading stays forever. The uploaded dataset was shown on the /galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy. The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading. Any configuration did I miss? Your feedback is highly appreciated. Hi Weihong, Sorry for the delayed response. Can you verify that the upload was not interrupted? Was the file in the tmp/ directory the same as the file you uploaded? Uploading huge files via a browser is not the most efficient way to get data into Galaxy. You may want to explore one of the other options in the wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP Note that the Upload via FTP method was designed for FTP but does not actually require that you use FTP. --nate Thank you! Weihong ___ 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/ ___ 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/
Re: [galaxy-dev] file upload issue
On Dec 15, 2011, at 4:39 PM, weihong yan wrote: Galaxy was configured with Apache as proxy server. The uploaded file size is very small. The message from paster.log related with it is POST /False?nginx_redir=/tool_runner/index HTTP/1.1 200 - http://galaxy.mcdb.ucla.edu/tool_runner?tool_id=upload1; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_2; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9 Hi, The message I just sent may be irrelevant as I missed this followup. It looks like you've configured the nginx upload options (or uncommented them) even though you are not using the nginx upload module? --nate Weihong --- On Thu, 12/15/11, Luciano Cosme cosme.sim...@gmail.com wrote: From: Luciano Cosme cosme.sim...@gmail.com Subject: Re: [galaxy-dev] file upload issue To: weihong yan weihong...@yahoo.com Cc: galaxy-dev@lists.bx.psu.edu Date: Thursday, December 15, 2011, 1:09 PM Hi, I am having the same issue today. It was working a few days ago, but now never finish uploading. Luciano On Dec 15, 2011, at 3:05 PM, weihong yan wrote: I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of Dataset is uploading stays forever. The uploaded dataset was shown on the /galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy. The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading. Any configuration did I miss? Your feedback is highly appreciated. Thank you! Weihong ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy with PBS runner Setting
On Dec 20, 2011, at 12:19 AM, Le-Shin Wu wrote: Thanks a million, Nate. I was able to submit my PBS job though galaxy. But I got another problem once the PBS job is finished. I submit a bowtie alignment testing job to our cluster by using PBS runner through galaxy. But I always got an error message showing on the right history panel as below. An error occurred running this job: # reads processed: 17214026 # reads with at least one reported alignment: 16405756 (95.30%) # reads that failed to align: 808270 (4.70%) Reported 16405756 alignments to 1 output stream(s) In fact, the message showing here is the output message from bowtie application and I did get the correct alignment result stored on galaxy server machine. Therefore, I tried adding some PBS options, such as -k eo or -j eo -o /dev/null, to the PBS runner in universe_wsgi.ini to remove the standard output message from bowtie. But this time I got the following error message. Hi Le-Shin, I am not familiar enough with bowtie to know why this error occurred. Perhaps someone else on the list can reply with some information. Please keep replies on the mailing list to ensure this is possible. An error occurred running this job:Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. It looks like if galaxy PBS runner did not receive the standard output from cluster, it will throw an error. Could you please help us to solve this problem. Thanks a lot. That's correct, Galaxy controls the location of the stdout/stderr files, changing these will cause such failures. --nate Le-Shin ___ 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/
Re: [galaxy-dev] Best practices with data on clusters
On Dec 20, 2011, at 5:04 AM, Cittaro Davide wrote: Hi developers, I have a question that may be an OT, but since galaxy can work in a clustered environment withh queueing system, I'll try to ask here. Is there anibody here who copies data in a local temporary directory before performing any analysis step and copy it back into the final results? Hi Davide, We did this for a while when we had a poorly performing fileserver. It can reduce load in that environment, but in cases where you are only going to read small portions of input files, you'll probably have longer execution time. Likewise if you'll simply be writing the output(s) in one big stream, since you then have to write it once locally and then back over the network. That said, if you have a lot interim steps that produce large data that then get merged via some process back to final outputs, it absolutely makes sense to use local disk for those steps (assuming local disk is large enough - another problem that we sometimes encounter). --nate Thanks d Sent from my iPad ___ 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/ ___ 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/
Re: [galaxy-dev] Problem uploading file by an URL
On Dec 20, 2011, at 8:48 AM, Marc Bras wrote: Hi, We have a Galaxy server in production and I have a problem when I want to download a huge file with HTTP URL. Galaxy starts well to download my file, but Galaxy writes this file in / tmp directory. Is it possible to change this directory ? Hi Marc, I'm not quite following your question. Are you saying that the file you are attempting to download from the Galaxy server is written to /tmp before being sent to your client (your web browser)? Or is the problem that when you upload a file via a URL in the URL/Text box on the upload form, the file is written to /tmp? If it's the latter, you can change this directory by setting $TEMP to the desired directory in the environment in which the Galaxy server starts. --nate Thank you, Regards, Marc Bras -- Marc Bras -- marc.b...@versailles.inra.fr INRA-URGI: Unité de Recherche Génomique Info Centre de Recherche de Versailles-Grignon Route de Saint Cyr 78026 Versailles - FRANCE Tel: +33 1 30 83 34 70 -- ___ 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/ ___ 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/
[galaxy-dev] Login problem
Hi all - I had this problem once before with a previous installation, and thought it was fixed, but I'm seeing it again and not sure its related. I have Galaxy running with a Proxy server on apache to get /galaxy instead of using port 8080. I've disabled load balancing and running everything in one process. I've set up the admin user using: admin_users = myem...@mydomain.edu then restarted Galaxy. I was already logged in, refreshed the page, and didn't see the Admin page, so I logged out. I tried to log back in but get redirected to the main galaxy page and I'm still not logged in. I checked the galaxy logs and see the following: serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 galaxy.web.framework DEBUG 2012-01-03 16:18:29,994 Error: this request returned None from get_history(): http://bic/galaxy/ 10.24.51.101 - - [03/Jan/2012:16:18:29 -0400] GET /galaxy/ HTTP/1.1 200 - - Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] GET /galaxy/root/tool_menu HTTP/1.1 200 - http://bic/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] GET /galaxy/history HTTP/1.1 200 - http://bic/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 galaxy.web.framework DEBUG 2012-01-03 16:18:30,594 Error: this request returned None from get_history(): http://bic/galaxy/root/user_get_usage 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] POST /galaxy/root/user_get_usage HTTP/1.1 500 - http://bic/galaxy/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 Error - type 'exceptions.AssertionError': Could not determine anonymous user's history. URL: http://bic/galaxy/root/user_get_usage File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 67 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 203 in user_get_usage return self.__user_get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 206 in __user_get_usage usage = trans.app.quota_agent.get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/quota/__init__.py', line 29 in get_usage assert history, Could not determine anonymous user's history. AssertionError: Could not determine anonymous user's history. CGI Variables - CONTENT_LENGTH: '-1' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a60ab36dc18d043e05577a892e93c9dadb26d3a1556c8c957dfed888be5af1bfd; galaxysession=c6ca0ddb55be603a1703b65966de4e010d7a3dd39f711df6d65d3ab9d5876cfd9280ce1808870f14' HTTP_HOST: 'bic' HTTP_ORIGIN: 'http://bic' HTTP_REFERER: 'http://bic/galaxy/history' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/root/user_get_usage' REMOTE_ADDR: '10.24.51.101' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'bic.cag.chop.edu' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration - __file__: '/home/galaxy/galaxy-dist/universe_wsgi.ini' admin_users: 'golh...@gmail.com' apache_xsendfile: 'True' cookie_path: '/galaxy' database_connection: 'postgres:///galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' debug: 'False' default_cluster_job_runner: 'pbs:///' enable_pages: 'True' here: '/home/galaxy/galaxy-dist' new_file_path: '/home/galaxy/galaxy-dist/database/tmp' nglims_config_file: 'tool-data/nglims.yaml' set_metadata_externally: 'True' start_job_runners: 'pbs' static_cache_time: '360' static_dir: '/home/galaxy/galaxy-dist/static/' static_enabled: 'True' static_favicon_dir: '/home/galaxy/galaxy-dist/static/favicon.ico' static_images_dir: '/home/galaxy/galaxy-dist/static/images' static_scripts_dir:
Re: [galaxy-dev] unpacking zip files during upload
On Dec 20, 2011, at 6:16 PM, Langhorst, Brad wrote: I'm working on unpacking a zip file into multiple datasets. I think this is the code path Upload.py UploadToolAction upload_common.py: get_uploaded_datesets new_upload new_history_upload or new_library_upload Then a job gets spooled Which calles add_file in data_source/upload.py And does the expansion of the zip I can unpack the zip and create files in the dataset's path there. But I don't know how to create more dataset associations, and I'm not sure that it makes sense to create datasets on the fly in data_source/upload.py . Should I pass some information along with data_source/upload.py about how to create dataset object and associate them with library/history associations? Or maybe I can pass in some kind of a callback that can handle the dataset expansion? (I'm pretty new to python, but it seems similar to ruby) Hey Brad, I was working on this a year or two ago and stopped working on the multi-file zip support. I forget all of the details, but I think the hangup had to do with creating associations when the tool runs, as you've found. This should most properly be done in the UploadToolAction, but then all of the dataset ids/filenames/etc need to be passed to the upload tool, and then have these datasets map to the right files when tools/data_source/upload.py expands the archive. It may be possible to use the method at the bottom of this page instead: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files I thought about a composite dataset, but that seems like overloading that concept. Really the files I'm thinking about uplaoding are 8 independent BAMs or fastqs or whatever – not a set of files that are related to each other. Composite would not be the right concept, since these should be considered unrelated files. Thanks for working on this! --nate Any suggestions? Brad -- Brad Langhorst New England Biolabs langho...@neb.com ___ 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/ ___ 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/
[galaxy-dev] Galaxy tool's error report
Hi, I'm executing a R script via Python's os.system() (using Rscript executable which allow executing R script in the command line). This script makes use of library that will attempt to load up Tcl/Tk interface. Though I don't see anything even if I'm running the commands on Windows interactive R console, it will attempt to connect to the display server unsuccessfully during Galaxy's execution (and fail because $DISPLAY is not set). The program runs just fine since I have the output I wanted. But Galaxy sees error, and I'm suspecting it's because of this DISPLAY thing. I don't understand how Galaxy detects something goes wrong. If anything I thought it's my Python script return code that should matter. But how does Galaxy know?! And how do I fix it? Timothy ___ 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/
Re: [galaxy-dev] Login problem
On Tue, Jan 3, 2012 at 4:21 PM, Ryan ngsbioinformat...@gmail.com wrote: Hi all - I had this problem once before with a previous installation, and thought it was fixed, but I'm seeing it again and not sure its related. I have Galaxy running with a Proxy server on apache to get /galaxy instead of using port 8080. I've disabled load balancing and running everything in one process. I've set up the admin user using: admin_users = myem...@mydomain.edu then restarted Galaxy. I was already logged in, refreshed the page, and didn't see the Admin page, so I logged out. I tried to log back in but get redirected to the main galaxy page and I'm still not logged in. I checked the galaxy logs and see the following: serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 galaxy.web.framework DEBUG 2012-01-03 16:18:29,994 Error: this request returned None from get_history(): http://bic/galaxy/ 10.24.51.101 - - [03/Jan/2012:16:18:29 -0400] GET /galaxy/ HTTP/1.1 200 - - Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] GET /galaxy/root/tool_menu HTTP/1.1 200 - http://bic/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] GET /galaxy/history HTTP/1.1 200 - http://bic/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 galaxy.web.framework DEBUG 2012-01-03 16:18:30,594 Error: this request returned None from get_history(): http://bic/galaxy/root/user_get_usage 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] POST /galaxy/root/user_get_usage HTTP/1.1 500 - http://bic/galaxy/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 Error - type 'exceptions.AssertionError': Could not determine anonymous user's history. URL: http://bic/galaxy/root/user_get_usage File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 67 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 203 in user_get_usage return self.__user_get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 206 in __user_get_usage usage = trans.app.quota_agent.get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/quota/__init__.py', line 29 in get_usage assert history, Could not determine anonymous user's history. AssertionError: Could not determine anonymous user's history. CGI Variables - CONTENT_LENGTH: '-1' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a60ab36dc18d043e05577a892e93c9dadb26d3a1556c8c957dfed888be5af1bfd; galaxysession=c6ca0ddb55be603a1703b65966de4e010d7a3dd39f711df6d65d3ab9d5876cfd9280ce1808870f14' HTTP_HOST: 'bic' HTTP_ORIGIN: 'http://bic' HTTP_REFERER: 'http://bic/galaxy/history' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/root/user_get_usage' REMOTE_ADDR: '10.24.51.101' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'bic.cag.chop.edu' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration - __file__: '/home/galaxy/galaxy-dist/universe_wsgi.ini' admin_users: 'golh...@gmail.com' apache_xsendfile: 'True' cookie_path: '/galaxy' database_connection: 'postgres:///galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' debug: 'False' default_cluster_job_runner: 'pbs:///' enable_pages: 'True' here: '/home/galaxy/galaxy-dist' new_file_path: '/home/galaxy/galaxy-dist/database/tmp' nglims_config_file: 'tool-data/nglims.yaml' set_metadata_externally: 'True' start_job_runners: 'pbs' static_cache_time: '360' static_dir: '/home/galaxy/galaxy-dist/static/' static_enabled:
Re: [galaxy-dev] Login problem
On Tue, Jan 3, 2012 at 4:21 PM, Ryan ngsbioinformat...@gmail.com wrote: Hi all - I had this problem once before with a previous installation, and thought it was fixed, but I'm seeing it again and not sure its related. I have Galaxy running with a Proxy server on apache to get /galaxy instead of using port 8080. I've disabled load balancing and running everything in one process. I've set up the admin user using: admin_users = myem...@mydomain.edu then restarted Galaxy. I was already logged in, refreshed the page, and didn't see the Admin page, so I logged out. I tried to log back in but get redirected to the main galaxy page and I'm still not logged in. I checked the galaxy logs and see the following: serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 galaxy.web.framework DEBUG 2012-01-03 16:18:29,994 Error: this request returned None from get_history(): http://bic/galaxy/ 10.24.51.101 - - [03/Jan/2012:16:18:29 -0400] GET /galaxy/ HTTP/1.1 200 - - Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] GET /galaxy/root/tool_menu HTTP/1.1 200 - http://bic/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] GET /galaxy/history HTTP/1.1 200 - http://bic/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 galaxy.web.framework DEBUG 2012-01-03 16:18:30,594 Error: this request returned None from get_history(): http://bic/galaxy/root/user_get_usage 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] POST /galaxy/root/user_get_usage HTTP/1.1 500 - http://bic/galaxy/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7 Error - type 'exceptions.AssertionError': Could not determine anonymous user's history. URL: http://bic/galaxy/root/user_get_usage File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 67 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 203 in user_get_usage return self.__user_get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 206 in __user_get_usage usage = trans.app.quota_agent.get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/quota/__init__.py', line 29 in get_usage assert history, Could not determine anonymous user's history. AssertionError: Could not determine anonymous user's history. CGI Variables - CONTENT_LENGTH: '-1' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a60ab36dc18d043e05577a892e93c9dadb26d3a1556c8c957dfed888be5af1bfd; galaxysession=c6ca0ddb55be603a1703b65966de4e010d7a3dd39f711df6d65d3ab9d5876cfd9280ce1808870f14' HTTP_HOST: 'bic' HTTP_ORIGIN: 'http://bic' HTTP_REFERER: 'http://bic/galaxy/history' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/root/user_get_usage' REMOTE_ADDR: '10.24.51.101' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'bic.cag.chop.edu' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration - __file__: '/home/galaxy/galaxy-dist/universe_wsgi.ini' admin_users: 'golh...@gmail.com' apache_xsendfile: 'True' cookie_path: '/galaxy' database_connection: 'postgres:///galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' debug: 'False' default_cluster_job_runner: 'pbs:///' enable_pages: 'True' here: '/home/galaxy/galaxy-dist' new_file_path: '/home/galaxy/galaxy-dist/database/tmp' nglims_config_file: 'tool-data/nglims.yaml' set_metadata_externally: 'True' start_job_runners: 'pbs' static_cache_time: '360' static_dir: '/home/galaxy/galaxy-dist/static/' static_enabled:
[galaxy-dev] tool_type=data_source_async
Hello all, I am trying to configure an Asynchronous tool (I can get it to work synchronously). My configuration looks something like this for the tool: ?xml version=1.0? tool name=mytoolname id=myunique_tool_id_1 tool_type=data_source_async descriptionmytool description/description command interpreter=pythondata_source.py $output $__app__.config.output_size_limit/command inputs action=http://myurl; check_values=false method=post displayGo to MyTool $GALAXY_URL/display /inputs request_param_translation request_param galaxy_name=URL_method remote_name=URL_method missing=post / request_param galaxy_name=URL remote_name=URL missing= / request_param galaxy_name=jobname remote_name=jobname missing=N/A / /request_param_translation uihints minwidth=800/ outputs data name=output format=zip / /outputs options sanitize=False refresh=True/ /tool This works fine and downloads the data, but I was expecting Galaxy to post another GALAXY_URL parameter for me to generate the data and than post back to Galaxy once done. This is described here... http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources However, I never receive “another” GALAXY_URL as descripbed in Step 1 of the Asynchronous data depositing section. I am using the most recent version of Galaxy. Can someone please show an example? Matt ___ 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/
