[galaxy-dev] Adding a new tag in galaxy
Hi All, I installed galaxy on local machine and i want to add a new tag in tool xml file .docs for adding new tag is not available in galaxy .if any one is working on it, plz help me in finding the solution .. Regards shashi --- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. --- ___ 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] List of browsers which supports galaxy
Hi, some browser are not supporting galaxy. if galaxy is supporting to specific version of browser in mozila ,IE,chrome,safari etc , can i get version number in mozila ,IE,chrome? if i have downloaded any new version of galaxy ,where will i get the list of supporting browser ? Regards shashi --- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. --- ___ 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-dev Digest
Hello there, Hope this is the right mailing list. Where can I find a detailed explanation of the track options when selecting a particular group in the UCSC main Table Browser. E.g: If I choose group: Genes and gene prediction track, what is the difference between the various tracks listed? The UCSC website does not give a detailed explanation of the differences between the various options. And outputs change depending on this. Thanks, Irene -- Irene, What you want is a tutorial for the UCSC table browser. Something like this will help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Clicking on the button 'describe table schema' provides additional information about the tracks's content. In the future, please email the galaxy-user mailing list with questions such as these. This email list goes to the entire Galaxy team and community, so you're likely to get quicker and more complete replies there. http://wiki.g2.bx.psu.edu/Mailing%20Lists Best, J. On Jul 8, 2012, at 6:28 AM, Irene Bassano wrote: Hi Jeremy, I am new with the Galaxy system and I was wondering if there is a web site which explains the possible options listed in group and track when loading data from UCSC. Depending on the group, the track changes: is there any manual that explains the difference between all these options? Many thanks, Irene From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu] Sent: Sunday, July 08, 2012 5:00 PM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 11 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: galaxy-dev Digest, Vol 73, Issue 10 (Dorset, Daniel C) 2. How to add tag in tool xml file (sshashi) -- Message: 1 Date: Sat, 7 Jul 2012 14:10:45 -0500 From: Dorset, Daniel C daniel.dor...@vanderbilt.edu To: Iry Witham iry.wit...@jax.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10 Message-ID: 9b568b41976b54469cc6e3fd758ef83105dbfe7...@its-drwnem10.ds.vanderbilt.edu Content-Type: text/plain; charset=us-ascii From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu] Sent: Saturday, July 07, 2012 11:00 AM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 10 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. pbs_python issues (Iry Witham) 2. Which css file does welcome.html use? (Dorset, Daniel C) 3. Re: Which css file does welcome.html use? (Jeremy Goecks) Hi Ira, I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, and I went through this
Re: [galaxy-dev] Galaxy Czars: Web conference Monday, July 9th 9 am
Hi Sebastian - Thanks for letting me know! You can please ignor those times. My meeting URL works dynamically to open up new web conferences. I just opened up the session - but I won't be back onto it until closer to 9 AM central time (Chicago/US) until 8:45am (in about 1 hour). Thanks, Ann On 7/9/2012 7:16 AM, Sebastian Schaaf wrote: Hi Ann, Just to be sure: you wrote that the web conference will take place at 9:00 AM Central Time (which should be 4:00 PM here in Munich). After clicking on the join meeting link to I was wondering that there the timepoint was noted as May 4, 2012 10:00 AM - May 3, 2013 11:00 AM (equals 5:00 PM here). Is this due to the daylight saving time or is there another reason for the one hour shift? Looking forward, thanks for the organization! Sebastian Ann Black-Ziegelbein schrieb: Thank you to everyone who helped provide doodle poll input for the first Czars web conference! We have set the date: *Date: *Monday, July 9th *Time: *09:00 AM Central Time* Web Conference (this will be recorded and posted for playback): *We will be using a Blackboard Collaborate web conference. See the section below for more tips on how to use Blackboard Collaborate (Elluminate Live) if you have not used it before. https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262330108904 * Agenda:* * Logistics: Address how we want to tackle these calls. Go over generic agenda. Frequency of calls * Presentation: Galaxy at Iowa: Discuss our issues with big data, how NGS tools take in/output data and finding the right storage server solution. * Group Goals: what do we want to accomplish with this group beyond discussions/sharing? * Open Mic recruit new volunteers for the next call. *Blackboard Collaborate (Ellumiate Live!) Tips: *For our web conferences we will try out Blackboard Collaborate web conferencing software. You do not need any special client, just a web browser and java installed (the client will run as a java web start app). You don't need to use a headset, but if you have one it does improve your audio. I will try to open up the session 15 minutes early for people to join and try out the technology. A couple of things to mention, when you launch your session - you can tune your connection speed: Talking works like a walkie-talkie ... you have to select Talk (see capture below) to open up your audio line. There can only be 6 simultaneous talkers. Please only select the talk button when you need to actually talk to reduce background noise and to free up lines for others to participate. Thanks! Ann Black-Ziegelbein University of Iowa ___ 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] pages problems - inserting one of many datasets
Firstly, thanks for Galaxy - it's great! I have a lot of items in various histories and I think I can reproduce what looks like 2 bugs in editing user pages, using either latest chrome and firefox on ubuntu 11.10 on Main First bug - cannot choose anything to insert to a page once the second or subsequent pages of multiple history items are showing when trying to insert a dataset into a page choose: User | saved pages Create a new page and edit content choose: insert a link to a galaxy object | insert dataset link A small window opens with the start of many pages of history items - the box is too small but if you scroll down you see Insert/Cancel action buttons Select the next page (#2) The small window opens up to the full screen - but the insert/cancel buttons are no longer there and you can scroll through the list of history items but you can't seem to get back to those buttons. Even from the second page, the browser back button takes me back to the edit page screen and the #1 link takes me back to the first page without any insert/cancel options. It seems that you can't select any dataset that's not on the first page to insert? Search can be used to limit the options and select a history item so I've managed to kind of get things to work bur ir sure isn't easy. Second bug: Once you've used the search option on the list of datasets, all the other pages of history items are gone - even if you remove the search term - it doesn't resume the paging mode properly so you have to go back to the main edit screen and start again. 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/
Re: [galaxy-dev] Galaxy Czars: Web conference Monday, July 9th 9 am
Hi Ann, Just to be sure: you wrote that the web conference will take place at 9:00 AM Central Time (which should be 4:00 PM here in Munich). After clicking on the join meeting link to I was wondering that there the timepoint was noted as May 4, 2012 10:00 AM - May 3, 2013 11:00 AM (equals 5:00 PM here). Is this due to the daylight saving time or is there another reason for the one hour shift? Looking forward, thanks for the organization! Sebastian Ann Black-Ziegelbein schrieb: Thank you to everyone who helped provide doodle poll input for the first Czars web conference! We have set the date: *Date: *Monday, July 9th *Time: *09:00 AM Central Time* Web Conference (this will be recorded and posted for playback): *We will be using a Blackboard Collaborate web conference. See the section below for more tips on how to use Blackboard Collaborate (Elluminate Live) if you have not used it before. https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262330108904 * Agenda:* * Logistics: Address how we want to tackle these calls. Go over generic agenda. Frequency of calls * Presentation: Galaxy at Iowa: Discuss our issues with big data, how NGS tools take in/output data and finding the right storage server solution. * Group Goals: what do we want to accomplish with this group beyond discussions/sharing? * Open Mic recruit new volunteers for the next call. *Blackboard Collaborate (Ellumiate Live!) Tips: *For our web conferences we will try out Blackboard Collaborate web conferencing software. You do not need any special client, just a web browser and java installed (the client will run as a java web start app). You don't need to use a headset, but if you have one it does improve your audio. I will try to open up the session 15 minutes early for people to join and try out the technology. A couple of things to mention, when you launch your session - you can tune your connection speed: Talking works like a walkie-talkie ... you have to select Talk (see capture below) to open up your audio line. There can only be 6 simultaneous talkers. Please only select the talk button when you need to actually talk to reduce background noise and to free up lines for others to participate. Thanks! Ann Black-Ziegelbein University of Iowa -- Sebastian Schaaf, M.Sc. Bioinformatics Chair of Biometry and Bioinformatics Department of Medical Information Sciences, Biometry and Epidemiology University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78229 ___ 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] Job output not returned from Cluster
Hi! Unfortunately I was not able to fix this problem yet. Is anybody out there who had a similar problem while using Galaxy with SGE or has the knowledge about the things I can look at? Thanks in advance! Cheers, Sascha ___ 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] Ability to Select SGE queue?
I'd like to provide a choice to my users which size Queue they would like to use when they are about to run a tool. I'm using the SGE configuration through DRMAA on my local install. I've only seen the queue set in the wsgi.ini file. Is there a way I can include this choice of SGE queue in my xml? Thanks Raymond Moore Informatics Specialist, Division of Biomedical Statistics Informatics | 507-293-0054 Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | www.mayoclinic.org http://www.mayoclinic.org/ ___ 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-dev Digest, Vol 73, Issue 10
Hi Daniel,
I did use -e previously. The ?e was a typo in my post. I ran it again
and it tries, but fails to generate the file(s) as shown:
:galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
fetch_one(): Trying to fetch:
http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz
fetch_one(): Fetched to:
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/archives/pbs_
python-4.1.0.tar.gz
unpack_source(): Unpacked to:
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-l
inux-x86_64-ucs4/pbs_python
copy_build_script(): Using build script
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/scripts/pbs_p
ython.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-l
inux-x86_64-ucs4/pbs_python:
/usr/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.eg
g
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.eg
g
checking for pbs-config... /usr/local/lib//../bin/pbs-config
Found torque version: 2.5.8
checking for python... /usr/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory...
${prefix}/lib64/python2.6/site-packages
checking for python extension module directory...
${exec_prefix}/lib64/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 -DNDEBUG -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -g -fwrapv -fPIC -DTORQUE_2_4
-I/usr/include/python2.6 -c src/pbs_wrap.c -o
build/temp.linux-x86_64-2.6/src/pbs_wrap.o
gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o
-L/usr/local/lib -L/usr/lib64 -ltorque -lpython2.6 -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/PBSQuery.py -
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/_pbs.so - build/bdist.linux-x86_64/egg
byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc
byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc
creating stub loader for _pbs.so
byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/PKG-INFO -
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/SOURCES.txt -
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/dependency_links.txt -
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/top_level.txt -
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding
'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Traceback (most recent call last):
File scripts/scramble.py, line 50, in module
egg.scramble()
File
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/scramble.py,
line 60, in scramble
raise ScrambleFailure( self, %s(): Egg build for %s did not appear to
fail, but no egg found to copy from expected
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
Hi, Greg,
I've still got issues after I downloaded the latest version from the dist
repository. So after I selected the datasets that I would like to transfer
from the sequencer and click the Transfer button, Galaxy generates an
error message : Invalid sample id (None)... I tried to delete this
dataset using the manage datasets menu, and Galaxy generates the same
error message: Invalid sample id (None). It seems galaxy system generates
the sample id automatically (the first one is sample_1), not sure why this
happens...
Luobin
On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Emily,
This issue should be resolved in change set 6924:12b14f3e78e9, which is
currently only available from our central repository. It will not be
available in the dist repository fro some time, so you'll have to pull it
from Galaxy central (https://bitbucket.org/galaxy/galaxy-central) if you
want it now.
Thanks very much for reporting this problem, and we apologize for the
inconvenience it caused.
Greg Von Kuster
On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote:
Hi Leandro,
I am also experiencing the same problem with the latest version of
galaxy. I just attempted to connect our sequencer for the first time
yesterday. I do not have an older version of galaxy to test and compare to
see if it works in earlier versions. I am able to transfer data from the
sequence to the import directory, however it is not moved to the data
library. My data_transfer.log also has the same error.
The server could not comply with the request since it is either
malformed or otherwise incorrect.
Does anyone have a solution for this?
Thanks
Emily
--
Message: 17
Date: Wed, 28 Mar 2012 13:15:47 +0200
From: Leandro Hermida soft...@leandrohermida.com
To: Luobin Yang yangl...@isu.edu
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs in
queue forever
Message-ID:
caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you Location
/ ... /Location container to not match URLs starting with /api. To
do this you have to change it to LocationMatch ^/(?!api)
/LocationMatch.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang yangl...@isu.edu wrote:
I've got the same problem and when I looked at the data_transfer.log, I
saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f',
u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample
status
from in queue to complete but didn't add the downloaded files to the
data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 -
Re: [galaxy-dev] Ability to Select SGE queue?
Thank you Peter, That's exactly what I was looking for. I'd really like to implement the functionality defined by John Chilton. The ability to select a queue based on the input size is very important to our group. Thanks again. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Monday, July 09, 2012 12:07 PM To: Moore, Raymond M. Cc: Galaxy Dev Subject: Re: [galaxy-dev] Ability to Select SGE queue? On Mon, Jul 9, 2012 at 5:34 PM, Moore, Raymond M. moore.raym...@mayo.edu wrote: I'd like to provide a choice to my users which size Queue they would like to use when they are about to run a tool. I'm using the SGE configuration through DRMAA on my local install. I've only seen the queue set in the wsgi.ini file. Is there a way I can include this choice of SGE queue in my xml? Thanks You can set the queue for each tool in the universe.xml file, but that is all at the moment AFAIK. More flexible options currently requires modification to Galaxy, e.g. http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html Peter ___ 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/
