Re: [galaxy-dev] finding parts of tool_conf.xml
I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration as a reference. Some of these components are installed via the tool shed, and others may have been manually added to main and are not included in the base tool_conf.xml.sample. I may be able to point you in the right direction, though -- what is it that you're trying to do? -Dannon On Tue, May 21, 2013 at 3:31 PM, vijayalakshmi vijira...@gmail.com wrote: Hi all, I am trying to get the *tool_conf.xml* section code corresponding to the following topics listed below. I am unable to find it in both the default build and the stable build in bitbucket. If you can point me to where I can find it, it'd be swell. 1) NGS: Variant detection 2) NGS: Picard(beta) 3) BEDTools 4) SnpEff Thanks, VJ. ___ 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] finding parts of tool_conf.xml
So tool_conf.xml only contains references to the other tool wrapper files. Those tools are either be in the distribution (which you can find in your galaxy-central/tools directory) or in the toolshed, at toolshed.g2.bx.psu.edu. -Dannon On Tue, May 28, 2013 at 1:32 PM, vijayalakshmi vijira...@gmail.com wrote: I am trying to integrate the following tools in galaxy but I am not able to find their corresponding code in the tool_conf.xml file. If you can point me to those, it'd we swell. 1) NGS: Variant detection 2) NGS: Picard(beta) 3) BEDTools 4) SnpEff Thanks, VJ. On Tue, May 28, 2013 at 12:42 PM, Dannon Baker dannon.ba...@gmail.comwrote: I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration as a reference. Some of these components are installed via the tool shed, and others may have been manually added to main and are not included in the base tool_conf.xml.sample. I may be able to point you in the right direction, though -- what is it that you're trying to do? -Dannon On Tue, May 21, 2013 at 3:31 PM, vijayalakshmi vijira...@gmail.comwrote: Hi all, I am trying to get the *tool_conf.xml* section code corresponding to the following topics listed below. I am unable to find it in both the default build and the stable build in bitbucket. If you can point me to where I can find it, it'd be swell. 1) NGS: Variant detection 2) NGS: Picard(beta) 3) BEDTools 4) SnpEff Thanks, VJ. ___ 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] Creating multiple datasets in a libset
Has the script created multiple histories? That's the intent, that each
file+workflow execution has a separate history.
And, for why that file vanished resulting in the exception -- is it
possible you ran a second instance of the script or moved the file?
-Dannon
On Wed, May 29, 2013 at 1:07 AM, neil.burd...@csiro.au wrote:
Further, when I look in the ~galaxy-dist/database/files/000 I can see both
files have been uploaded but only the second file has a history associated
to it
Thanks
Neil
-Original Message-
From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Wednesday, 29 May 2013 2:45 PM
To: galaxy-dev@lists.bx.psu.edu; 'Dannon Baker'; 'robert.lecl...@gmail.com
'
Subject: Re: Creating multiple datasets in a libset
Hi Guys,
Did you manage to get multiple datasets working? I can't seem to
upload multiple files. Only the last file appears in the history. I changed
my code as mentioned in the thread below in example_watch_folder.py to
add multiple files separated by a new line and increased the sleep time:
for fname in os.listdir(in_folder):
fullpath = os.path.join(in_folder, fname)
print ' fullpath is [%s] ' % fullpath
if os.path.isfile(fullpath):
data = {}
data['folder_id'] = library_folder_id
data['file_type'] = 'auto'
data['dbkey'] = ''
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] =
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T1_Screening.nii.gz\n
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz
print ' data is [%s] ' % str(data['filesystem_paths'])
data['create_type'] = 'file'
libset = submit(api_key, api_url + libraries/%s/contents
% library_id, data, return_formatted = False)
#TODO Handle this better, but the datatype isn't always
# set for the followup workflow execution without this
# pause.
time.sleep(65)
However, I get the following crash:
./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c
http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input
/home/galaxy/galaxy-drop/output This One f2db41e1fa331b3e
fullpath is
[/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz]
data is [/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T1_Screening.nii.gz
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz]
url is :
http://barium-rbh/csiro/api/libraries/33b43b4e7093c91f/contents?key=64f3209856a3cf4f2d034a1ad5bf851c
data is : {'file_type': 'auto', 'dbkey': '', 'create_type': 'file',
'folder_id': 'F33b43b4e7093c91f', 'upload_option': 'upload_paths',
'filesystem_paths':
'/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T1_Screening.nii.gz\n
/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz'}
url is :
http://barium-rbh/csiro/api/workflows?key=64f3209856a3cf4f2d034a1ad5bf851c
data is : {'workflow_id': 'f2db41e1fa331b3e', 'ds_map': {'14': {'src':
'ld', 'id': 'ff5476bcf6c921fa'}}, 'history':
'141_S_0851_MRI_T2_Screening.nii.gz - apiFullCTE'}
{'outputs': ['daecbdd824e1c349', '358eb58cd5463e0d', 'c0279aab05812500'],
'history': '3cc0effd29705aa3'} url is :
http://barium-rbh/csiro/api/workflows?key=64f3209856a3cf4f2d034a1ad5bf851c
data is : {'workflow_id': 'f2db41e1fa331b3e', 'ds_map': {'14': {'src':
'ld', 'id': '79966582feb6c081'}}, 'history':
'141_S_0851_MRI_T2_Screening.nii.gz - apiFullCTE'}
{'outputs': ['19c51286b777bc04', '0f71f1fc170d4ab9', '256444f6e7017e58'],
'history': 'b701da857886499b'} Traceback (most recent call last):
File ./example_watch_folder.py, line 89, in module
main(api_key, api_url, in_folder, out_folder, data_library, workflow )
File ./example_watch_folder.py, line 75, in main
shutil.move(fullpath, os.path.join(out_folder, fname))
File /usr/lib/python2.7/shutil.py, line 299, in move
copy2(src, real_dst)
File /usr/lib/python2.7/shutil.py, line 128, in copy2
copyfile(src, dst)
File /usr/lib/python2.7/shutil.py, line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-drop/input/141_S_0851_MRI_T2_Screening.nii.gz'
It says there is no such file, but this file has already been copied from
the input to the output directory. Any help much appreciated
Neil
--
Message: 2
Date: Mon, 29 Apr 2013 16:11:39 -0400
From: Rob Leclerc robert.lecl...@gmail.com
To: Dannon Baker dannon.ba...@gmail.com
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Creating multiple datasets in a libset
Message-ID:
CAGkd85fHSgO2YC1T+Frctyso9G5rfQb=_mLyHGSdxPM+s3=
8...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Dannon,
I've written some code to (i) query a dataset to ensure that it's been
uploaded after
Re: [galaxy-dev] php script integration query
As long as you're able to execute your php script from the command line, it should work fine. -Dannon On Wed, May 29, 2013 at 7:25 AM, Prasun Dutta prasundutt...@yahoo.co.inwrote: Hi, If I have some programs in php which I need to integrate in Galaxy as a tool, can I do it? I know if I have some programs written in Perl, python,java,C or C++, I can easily integrate them. Can I do the same with a php script? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK ___ 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] advice on a mixed cloud/SGE architecture
Ok, got it. Unfortunately this isn't really possible at this time, at least not without a lot of hacking and dealing with data staging issues and delays (in downloading data from S3 to local cluster to work, uploading results back to galaxy server, etc.). Galaxy, with the exception of the LWR - http://wiki.galaxyproject.org/Admin/Config/LWR, relies on a shared filesystem between the galaxy instance and workers. I'd really recommend colocating Galaxy with the cluster, at least for now. We do want to build out the ability to use EC2 as an expansion to local clusters, but I imagine it working the other way around -- that is, you have a local instance that uses S3 as permanent storage and spin up extra nodes in EC2 to handle excess load as necessary. -Dannon On Tue, May 28, 2013 at 1:14 PM, Nikolay N. nikola...@gmail.com wrote: Hi Dannon, Yes, this is what I was thinking about. The reason is that at the moment the SGE cluster is managed separately. Also we are likely to migrate to a different cluster infrastructure (probably LSF) and I thought that if I set up a master node on AWS I could than only have to change the cluster part. The idea is that if the user metadata is stored on the AWS master node and his/her files on S3 than it would be relatively easy to just swap the cluster that is providing the raw muscle. But I don't have a good understanding of the galaxy architecture and the documentation seems a bit sparse. So any advice on this is most welcome. -Nick On Tue, May 28, 2013 at 3:58 PM, Dannon Baker dannon.ba...@gmail.comwrote: Hi Nick, Not sure I completely understand what you're trying to do here. So, you want to have a galaxy head node on AWS that dispatches jobs to a non-AWS private SGE cluster? -Dannon On Thu, May 16, 2013 at 12:18 PM, Nikolay N. nikola...@gmail.com wrote: Hi, I was contemplating setting up a galaxy master node on a aws instance but executing the workflows on an internal SGE cluster. I am not yet very familiar with galaxy so wanted to ask whether this is feasible (i.e. the API would support it). Any advice/recommendation is most welcome. many thanks, Nick ___ 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] Status of Galaxy Cloud Instance dev
No firm release set for the new cloudman yet, but you can always follow development here: https://trello.com/board/galaxy-cloudman/5136209e9beefacb77004e6d There are a few final issues we're wrapping up before we can release, but we're hoping it'll be soon. On Fri, May 31, 2013 at 7:31 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, I am planning to launch a Galaxy Cloud Instance, to run for about one month. But I believe I've read somewhere a new image of Galaxy on AWS is being prepared right now. Can somebody update me on the status? Perhaps it is smart to wait a few days with launching through CloudLaunch until the new release is there? Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.**php/about/80-teamhttp://www.bits.vib.be/index.php/about/80-team __**_ 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/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] Status of Galaxy Cloud Instance dev
On Fri, May 31, 2013 at 9:51 AM, John Chilton chil...@msi.umn.edu wrote: Could you enable comments for non-board members like the Galaxy Development Trello allows? Of course, actually thought I'd already done that. Fixed! ___ 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] Installation of 20130603 Galaxy image with MySQL fails
Hi Linda,
The decorator issue should be resolved in galaxy-central now. I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.
Thanks!
-Dannon
On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:
Hi. I am new to the Galaxy forum and I am trying to setup a new local
Galaxy instance with MySQL on RH6.2 x86_64.
On a newly installed OS node, using the hg clone command (hg clone *
https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist)
which gets the current Galaxy 20130603 image, I am getting the following
errors when running run.sh:
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173,
in execute
self.errorhandler(self, exc, value)
File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
in key specification without a key length) 'CREATE INDEX ix_history_slug
ON history (slug)' ()
Reading the forum, someone stated it can be bypass by running the CREATE
INDEX.
mysql CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0 Duplicates: 0 Warnings: 0
When trying to run.sh again after the CREATE INDEX, will get this error:
File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py,
line 52, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
line 107, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg
) )
Exception: Your database has version '29' but this code expects version
'115'. Please backup your database and then migrate the schema by running
'sh manage_db.sh upgrade'.
So try to run the sh manage_db.sh upgrade' now will get this error:
$ sh manage_db.sh upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 13, in module
from migrate.versioning.shell import main
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
line 12, in module
from migrate.versioning import api
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
line 33, in module
from migrate.versioning import (repository, schema, version,
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
line 13, in module
from migrate.versioning import version, pathed, cfgparse
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
line 10, in module
from migrate.versioning import pathed, script
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
line 11, in module
from migrate.versioning.util import KeyedInstance
File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
line 7, in module
from decorator import decorator
ImportError: No module named decorator
In some searches, there were tips of deleting the eggs directory and rerun
run.sh or use a python env. Neither option worked.
Was not able to find anything meaningful about the decorator error.
Note:, I was able to get Galaxy up with MySQL using the Galaxy
788cd3d06541 image on a different node. So I am thinking maybe it is the
new 20130603 image that is giving me issues?
Commands used to get Galaxy up:
Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1]
python version [2.6.6]
Grant ALL PRIVILEGES galaxy_db.* TO galaxy_user on localhostname with
PWD
Images tested:
*Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image Did not
run the hg update command. [This worked]
*hg clone stable of newest image [Failed]
Update the universe_wsg.ini with the port, host, database_connection
to mysql
Ran run.sh
Thanks.
Linda
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Re: [galaxy-dev] Issue with set_user_disk_usage.py and Postgres 8.x
Thanks for the bug fix, (and for the reminder that it was still sitting in the inbox, sorry about that). I've verified the fix as well and pulled it into -central. -Dannon On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons lpars...@princeton.eduwrote: Thanks for confirmation Björn. Pull request was submitted: https://bitbucket.org/galaxy/galaxy-central/pull-request/97/fix-for-postgres-versions-9/diff Trello card also created: https://trello.com/c/Z0EynAV2 Björn Grüning wrote: Hi Lance, I can confirm both the regression and the fix. A pull request would be great I think. I can also do it if you want. Thanks, Björn The recent updates to set_user_disk_usage.py for Postgres users have an issue with Postgres 8.x. The SQL in the pgcalc method (line 51) leads to the following error: sqlalchemy.exc.ProgrammingError: (ProgrammingError) column d.total_size must appear in the GROUP BY clause or be used in an aggregate function LINE 4: FROM ( SELECT d.total_siz... ^ The problem is that version of Postgres before 9.x were a bit more restrictive in the use of GROUP BY. This can be fixed using DISTINCT ON instead. See this StackOverflow post for more info:http://stackoverflow.com/questions/1769361/postgresql-group-by-different-from-mysql I've included a patch below. Let me know if a pull request would be preferred. --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -52,7 +52,7 @@ sql = UPDATE galaxy_user SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) - FROM ( SELECT d.total_size + FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id FROM history_dataset_association hda JOIN history h ONh.id = hda.history_id JOIN dataset d ON hda.dataset_id = d.id @@ -62,7 +62,7 @@ AND d.purged = false AND d.id NOT IN (SELECT dataset_id FROM library_dataset_dataset_association) -GROUP BY d.id) sizes) +) sizes) WHERE id = :id RETURNING disk_usage; -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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] bug in galaxy-central security
That'll work, but it'll deactivate select2 across the board for all pages
in your galaxy instance. I committed a fix for those specific admin pages
yesterday, available in galaxy-central (stable as well as default branch).
-Dannon
On Thu, Jun 6, 2013 at 1:37 PM, Robert Baertsch baert...@soe.ucsc.eduwrote:
Hi Dannon,
I deleted the declaration to select2 in base.mako (line 42) and that fixed
the problem for now. (thanks to Ted for the tip!)
-Robert
On Jun 4, 2013, at 1:30 PM, Dannon Baker wrote:
Hey Robert,
Thanks for catching this; I'm working on getting a fix out (this affects
multiple areas in the admin panel) but if you need to temporarily fix a
single page to get things working you can execute
$('select').select2(destroy) in your javascript console.
-Dannon
On Tue, Jun 4, 2013 at 3:20 PM, Robert Baertsch baert...@soe.ucsc.eduwrote:
James,
I upgraded to the latest galaxy-central and starting with a blank
database. When I add more than 20 users, the security group admin screen
doesn't populate.
mako is pulling the correct data but there is some jquery code for
autocomplete or search that seems to be having trouble.
Here is a screen shot. Let me know if you want admin access to this
server and I'll setup a user for you.
-Robert
Screen Shot 2013-06-04 at 12.18.21 PM.png
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Re: [galaxy-dev] local install problem
How did you install your python, or are you using the default ubuntu 12.04 version? The bz2 module should be distributed with any python since 2.3. -Dannon On Thu, Jun 6, 2013 at 3:25 PM, Andrew Krohn alk...@nau.edu wrote: I looked through others' problems, but this seems unique. I just did a clean install of Ubuntu 12.04 and wanted to add Galaxy to integrate our various pipelines (16S rRNA via qiime, RADseq data, small genome assemblies). However, I seem to be stuck at the beginning of the install. Followed instructions from this page explicitly ( http://wiki.galaxyproject.org/Admin/Get%20Galaxy). When I run sh run.sh, I get the below output, and the server cannot be accessed via web browser. I am using python 2.7.3. I opened a python instance and ran import bz2, but then I get the same error (ImportError: No module named bz2). enggen@OptimusPrime:~/galaxy-dist$ sh run.sh Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 1049, in run invoke(command, command_name, options, args[1:]) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 1055, in invoke exit_code = runner.run(args) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 220, in run result = self.command() File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /home/enggen/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /home/enggen/galaxy-dist/lib/galaxy/web/buildapp.py, line 3, in module from galaxy.webapps.galaxy.buildapp import app_factory File /home/enggen/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 17, in module import galaxy.model File /home/enggen/galaxy-dist/lib/galaxy/model/__init__.py, line 23, in module import galaxy.datatypes.registry File /home/enggen/galaxy-dist/lib/galaxy/datatypes/registry.py, line 5, in module import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex File /home/enggen/galaxy-dist/lib/galaxy/datatypes/tabular.py, line 14, in module from galaxy.datatypes.checkers import is_gzip File /home/enggen/galaxy-dist/lib/galaxy/datatypes/checkers.py, line 1, in module import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr ImportError: No module named bz2 Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen ___ 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] local install problem
For whatever reason, it looks like your python was compiled without bz2 support. The following links may help you get a usable python installed: http://stackoverflow.com/questions/12806122/missing-python-bz2-module http://stackoverflow.com/questions/8115280/importerror-no-module-named-bz2-for-python-2-7-2 On Thu, Jun 6, 2013 at 4:19 PM, Andrew Krohn alk...@nau.edu wrote: I am using the default ubuntu 12.04 python. Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen On Thu, Jun 6, 2013 at 1:17 PM, Dannon Baker dannon.ba...@gmail.comwrote: How did you install your python, or are you using the default ubuntu 12.04 version? The bz2 module should be distributed with any python since 2.3. -Dannon On Thu, Jun 6, 2013 at 3:25 PM, Andrew Krohn alk...@nau.edu wrote: I looked through others' problems, but this seems unique. I just did a clean install of Ubuntu 12.04 and wanted to add Galaxy to integrate our various pipelines (16S rRNA via qiime, RADseq data, small genome assemblies). However, I seem to be stuck at the beginning of the install. Followed instructions from this page explicitly ( http://wiki.galaxyproject.org/Admin/Get%20Galaxy). When I run sh run.sh, I get the below output, and the server cannot be accessed via web browser. I am using python 2.7.3. I opened a python instance and ran import bz2, but then I get the same error (ImportError: No module named bz2). enggen@OptimusPrime:~/galaxy-dist$ sh run.sh Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 1049, in run invoke(command, command_name, options, args[1:]) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 1055, in invoke exit_code = runner.run(args) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 220, in run result = self.command() File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /home/enggen/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /home/enggen/galaxy-dist/lib/galaxy/web/buildapp.py, line 3, in module from galaxy.webapps.galaxy.buildapp import app_factory File /home/enggen/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 17, in module import galaxy.model File /home/enggen/galaxy-dist/lib/galaxy/model/__init__.py, line 23, in module import galaxy.datatypes.registry File /home/enggen/galaxy-dist/lib/galaxy/datatypes/registry.py, line 5, in module import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex File /home/enggen/galaxy-dist/lib/galaxy/datatypes/tabular.py, line 14, in module from galaxy.datatypes.checkers import is_gzip File /home/enggen/galaxy-dist/lib/galaxy/datatypes/checkers.py, line 1, in module import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr ImportError: No module named bz2 Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen ___ 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
Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Hi Linda, Sorry I wasn't clear before. The fix for that first issue is in galaxy-central's stable branch, which will be migrated to galaxy-dist probably sometime next week. You can always pull directly from -central though, using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central/' That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. -Dannon On Wed, Jun 5, 2013 at 4:47 PM, Linda Cham lc...@us.ibm.com wrote: Hi Bjorn, Currently seen $ hg tip changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 Removed galaxy-dist directory and rerun the hg clone command. $ hg clone *https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist destination directory: galaxy-dist requesting all changes adding changesets adding manifests adding file changes added 9851 changesets with 36400 changes to 7175 files updating to branch stable 4132 files updated, 0 files merged, 0 files removed, 0 files unresolved $ cd galaxy-dist $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg pull ; hg update stable pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found 0 files updated, 0 files merged, 0 files removed, 0 files unresolved Check the script/manage_db.py: from galaxy import eggs - No decorator line eggs.require( Tempita ) eggs.require( SQLAlchemy ) eggs.require( sqlalchemy_migrate ) $ hg update tip 0 files updated, 0 files merged, 0 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg update default 82 files updated, 0 files merged, 2 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 script/manage_db.py still the same as above. [image: Inactive hide details for Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, Hi Dannon,]Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, Hi Dannon, From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: Dannon Baker dannon.ba...@gmail.com, Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/05/2013 04:30 PM Subject: Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails -- Hi Linda, Hi Dannon, Thanks. I tried to do the hg pull and update and hg tip but I do not see the changes in my working directory. So I added the one liner eggs.require( decorator ) to scripts/manage_db.py. Ran the sh manage_db.sh upgrade and get this error: that is really strange. Can you show us what the output of hg tip is? Do you mind to start with a fresh checkout and that particular change? Thanks, Björn graycol.gif___ 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] bug in galaxy-central security
Thanks, fixed in 9972:7794e02d5ee5.
-Dannon
On Fri, Jun 7, 2013 at 2:26 AM, Robert Baertsch baert...@soe.ucsc.eduwrote:
Dannon,
Can you also apply the same select2 fix to:
templates/webapps/galaxy/library/common/library_permissions.mako
It has the same problem.
-Robert
On Jun 6, 2013, at 10:42 AM, Dannon Baker wrote:
That'll work, but it'll deactivate select2 across the board for all pages
in your galaxy instance. I committed a fix for those specific admin pages
yesterday, available in galaxy-central (stable as well as default branch).
-Dannon
On Thu, Jun 6, 2013 at 1:37 PM, Robert Baertsch baert...@soe.ucsc.eduwrote:
Hi Dannon,
I deleted the declaration to select2 in base.mako (line 42) and that
fixed the problem for now. (thanks to Ted for the tip!)
-Robert
On Jun 4, 2013, at 1:30 PM, Dannon Baker wrote:
Hey Robert,
Thanks for catching this; I'm working on getting a fix out (this affects
multiple areas in the admin panel) but if you need to temporarily fix a
single page to get things working you can execute
$('select').select2(destroy) in your javascript console.
-Dannon
On Tue, Jun 4, 2013 at 3:20 PM, Robert Baertsch baert...@soe.ucsc.eduwrote:
James,
I upgraded to the latest galaxy-central and starting with a blank
database. When I add more than 20 users, the security group admin screen
doesn't populate.
mako is pulling the correct data but there is some jquery code for
autocomplete or search that seems to be having trouble.
Here is a screen shot. Let me know if you want admin access to this
server and I'll setup a user for you.
-Robert
Screen Shot 2013-06-04 at 12.18.21 PM.png
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Re: [galaxy-dev] minor SQLAlchemy PostgreSQL issue
Even though the dialect name changed, the existing database urls should be compatible (postgres:///...). Did you find this not to be the case? -Dannon On Mon, Jun 10, 2013 at 12:54 PM, Richard Burhans r...@bx.psu.edu wrote: The SQLAlchemy postgres dialect was renamed to postgresql. Changing: database_connection = postgres:///... to: database_connection = postgresql:/// in the ini file causes Galaxy (tool_shed in my case) to fail to start as the postgres dialect is mentioned by name a few places in the code. Not a big deal, but I figured I'd report it. -rico __**_ 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/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] database upgrade crashes after upgrade to the June 3, 2013 Galaxy release
Christophe, Glad it's working. The updates should merge seamlessly so you shouldn't need to do anything else when you update again. That said, for future use, you can swap branches like: 'hg update stable' to swap to the stable branch. If you're on galaxy-dist, you can still pull (and update) from the stable branch in galaxy-central using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central'. -Dannon On Wed, Jun 12, 2013 at 5:33 PM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Thank you so much Björn, I made the change of the file directly by hand (not sure to be able to cleanly switch to default from stable with the new mercurial mode) and it worked. Chris 2013/6/12 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de Hi Christophe, can you try to update to the latest revision? It is fixed here: https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e Cheers, Bjoern Hi, Sorry to bother again, but we have now a problem with the last release of galaxy-dist The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115' sh manage_db.sh upgrade Traceback (most recent call last): File ./scripts/manage_db.py, line 13, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py, line 12, in module from migrate.versioning import api File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py, line 33, in module from migrate.versioning import (repository, schema, version, File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py, line 13, in module from migrate.versioning import version, pathed, cfgparse File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py, line 10, in module from migrate.versioning import pathed, script File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py, line 11, in module from migrate.versioning.util import KeyedInstance File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py, line 7, in module from decorator import decorator ImportError: No module named decorator Any idea ? Thanks Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.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/ 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] moving galaxy published pages
Hi Vipin, There isn't currently a page export/import mechanism and the steps outlined above seem reasonable. Of course, contributions are appreciated should anyone wish to undertake this project. -Dannon On Thu, Jun 13, 2013 at 5:27 PM, Vipin TS vipin...@gmail.com wrote: Hello dev-team, Usually when I want to move a Galaxy Published Page between instances I follows these steps: (a) moving workflows and dataset from instance_1 to instance_2 (b) run the workflow at instance_2 (c) create the page at instance_2 So my question is - Can I move/share published pages between instances other than the above way just curious to know, --/Vipin ___ 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] How to speed up submissions of workflows
The web process is definitely the bottleneck right now, creating more should improve things. I'd guess it wouldn't speed up any individual submission, but it'd allow you to submit several at once. Lastly, this is a known issue that we're hoping to resolve with a rewrite of the workflow dispatching mechanism. -Dannon On Fri, Jun 14, 2013 at 2:17 PM, Thon Deboer thondeb...@me.com wrote: Hi, ** ** I am routinely running hundreds of pair-end sequencing runs and find that STARTING a workflow on all of these can easily take hours since it seems each workflow preparation takes about 3 minutes, so for doing 128 fastq pairs like this it will take over 3 hours just to get all workflows running…. ** ** Is there any way for me to speed up this process, maybe by adding more handlers (although I am suspecting the WEB server is the bottleneck here)? I already run 8 handlers but only one web server… I could loadbalance the webservers through my proxy server…Will that speed up the submissions or are we stuck with this linear process? Thanks, ** ** Thon ** ** ___ 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] 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/
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':
Re: [galaxy-dev] Galaxy setup from cloudman shows no tools in the tool panel
This is actually a bug in the current tip of galaxy-central that we should have resolved shortly. We should have an update out today, or you can downgrade your galaxy to revision dfba9b0 (hg update -r dfba9b0). -Dannon On Tue, Jun 18, 2013 at 8:12 AM, Marco Ocana moc...@broadinstitute.orgwrote: Hi, Just setup Galaxy using cloudman on AWS. I updated the version of Galaxy using the Admin Console (it shows revision 10066:d2d4b6ac2139http://bitbucket.org/galaxy/galaxy-central/changesets/d2d4b6ac2139 ). I also did the additional tool installation described in the Galaxy log file by running the script: sh ./scripts/migrate_tools/0007_tools.sh install_dependencies FInally, I added the genomespace tools as described in: http://wiki.galaxyproject.org/GenomeSpace From the cloudman admin console all systems appear as Running . However, when I go to the Galaxy main page, the Tools panel is completely empty. I tried restarting Galaxy from the cloudman console a couple of times. There are errors that show up in the Galaxy log, though none that could tell me precisely what I should do to get the tools to display. I have attached the Galaxy log file. Any help would be appreciated. Thanks Marco ___ 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] Galaxy setup from cloudman shows no tools in the tool panel
This should now be resolved in -central. If you update again, you'll get the changes and your instance should work fine. -Dannon On Tue, Jun 18, 2013 at 8:34 AM, Dannon Baker dannon.ba...@gmail.comwrote: This is actually a bug in the current tip of galaxy-central that we should have resolved shortly. We should have an update out today, or you can downgrade your galaxy to revision dfba9b0 (hg update -r dfba9b0). -Dannon On Tue, Jun 18, 2013 at 8:12 AM, Marco Ocana moc...@broadinstitute.orgwrote: Hi, Just setup Galaxy using cloudman on AWS. I updated the version of Galaxy using the Admin Console (it shows revision 10066:d2d4b6ac2139http://bitbucket.org/galaxy/galaxy-central/changesets/d2d4b6ac2139 ). I also did the additional tool installation described in the Galaxy log file by running the script: sh ./scripts/migrate_tools/0007_tools.sh install_dependencies FInally, I added the genomespace tools as described in: http://wiki.galaxyproject.org/GenomeSpace From the cloudman admin console all systems appear as Running . However, when I go to the Galaxy main page, the Tools panel is completely empty. I tried restarting Galaxy from the cloudman console a couple of times. There are errors that show up in the Galaxy log, though none that could tell me precisely what I should do to get the tools to display. I have attached the Galaxy log file. Any help would be appreciated. Thanks Marco ___ 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] Clone Galaxy from repository: mercurial from behind proxy?
On Tue, Jun 18, 2013 at 10:54 AM, Sebastian Schaaf sch...@ibe.med.uni-muenchen.de wrote: Thus, the cloning process as the LDAP user (did not want to store the foreign username/password explicitly in the galaxy user files) worked, although I get this message: *** failed to import extension hgext.imerge: no module named imerge (once at the process' beginning and once at the end) Anyway, this seems to be more a warning than an error. I found possibility to silence it, but would like to understand what the missing may cause. Any clue, anyone? Imerge is an old extension that used to ship with mercurial. Check your .hgrc file for the [extensions] section and make sure there's no line for imerge. If there is, remove it -- recent versions of mercurial don't use this anymore. ___ 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] Installation of 20130603 Galaxy image with MySQL fails
Hi Jean-François, The index issues preventing a new instance from starting are resolved in the stable branch of galaxy-central; if you pull updates from that branch you should be able to start a new instance. While the instance will start and run, there are other peculiarities I still need to resolve and I'd really recommend using postgres for a new instance at this time if you're at all able to do so. -Dannon On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly jean-francois.t...@crg.eu wrote: Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));) Thx a lot for your help Best Jean-François On 06/05/2013 05:12 PM, Linda Cham wrote: Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone * https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used in key specification without a key length) 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 -- # Jean-François Taly Bioinformatician Bioinformatics Core Facilityhttp://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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] [galaxy-user] Problems when downloading a local galaxy tool (old version)
Hsiong, Could you try 'hg clone --verbose --debug https://bitbucket.org/galaxy/galaxy-dist/' to see if we get more useful error output? If it passed the warning and went ahead and got all the changes then I'm not sure if that's an issue. Also, I'm swapping this thread to the galaxy-dev list, since it's about installing a local instance. -Dannon On Sun, Jun 23, 2013 at 1:15 AM, xiong lynhsi...@hotmail.com wrote: ** Dear friends: As a locally installed Genomic-hyperbrowser need a rather old version of Galaxy, I runed the command hg clone https://bitbucket.org/galaxy/galaxy-dist/ -u 26920e20157f galaxy-dist-hb according to the website http://hyperbrowser.uio.no/hb/static/download.html. However, the hg did not download successfully, but reported warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) destination directory: galaxy-dist-hb requesting all changes adding changesets and this information on the screen mainteined (at least half a day unless I hit ctrl+Z and kill the job) without any other errors (still in the destination directory it generated a nearly empty dir galaxy-dist-hb containing a filefold named .hg”——one store filefold and several small files included). My mercurial version is 2.6, and I use Xshell to reach CentOS Server. Actually, even I downloaded the latest version of galaxy (hg clone https://bitbucket.org/galaxy/galaxy-dist/), it also reported the same information on the screen. On the other hand, I can get the latest tarballs of galaxy, but it can not be updated to an old version. Please give me some clues about problems above, and any ideas to get tarballs for an old version? Thanks in advance! Hsiong ___ 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/ 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] nglims/removing multiplexing
It's that previous versions of sqlalchemy-migrate didn't clean up these tables under sqlite and didn't mind overwriting them if they existed, but the new version both does clean up after itself, and expects the table to not exist, failing miserably if it does. I think there's a Trello card for fixing this somewhere, but yes, the temporary workaround is to just drop the migration_tmp table if this happens and migrate again. On Jul 1, 2013, at 3:16 PM, Brad Chapman chapm...@50mail.com wrote: Lee; Thanks Brad! I updated with hg pull -u and then ran sh manage_db.sh upgrade but I have an error. Could you help? I backed up my database before I ran the upgrade script, so I can go back in time. I think there is something funky going on with the version of SQLAlchemy-migrate currently in use in Galaxy, at least on SQLite databases. It creates temporary tables but then they are not getting cleaned up. The best fix is to reset yourself back to the original version (minus 1 to take into account the LIMS tables): sh manage_db.sh downgrade --version=108 Then redo the upgrade: sh manage_db.sh uprade Anytime you run into the intermittent error, you can manually fix with: $ sqlite3 database/universe.sqlite sqlite drop table migration_tmp; Keep your backup around and you can do this with the new version. Sorry for the ugly hack but that was a reasonable workaround. There is some discussion on the mailing list about this previously but I don't think there was a good conclusion: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014570.html Hope this cleans it up for you, Brad (sorry about the wall of text) 109 - 110... /home/galaxy/bin/chapman-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py:723: SAWarning: Did not recognize type 'BIGINT' of column 'bytes' Add UUID column to dataset table done 110 - 111... Add support for job destinations to the job table done 111 - 112... Migration script to add the data_manager_history_association table and data_manager_job_association. 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,549 Created data_manager_history_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,549 Created data_manager_history_association table Created data_manager_history_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,890 Created data_manager_job_association table 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,890 Created data_manager_job_association table Created data_manager_job_association table done 112 - 113... Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. done 113 - 114... Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. done 114 - 115... Altering password column failed Traceback (most recent call last): File lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py, line 15, in upgrade user.c.password.alter(type=String(255)) File /home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py, line 491, in alter return alter_column(self, *p, **k) File /home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py, line 136, in alter_column engine._run_visitor(visitorcallable, delta) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 2302, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1972, in _run_visitor **kwargs).traverse_single(element) File /home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py, line 53, in traverse_single ret = super(AlterTableVisitor, self).traverse_single(elem) File build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py, line 106, in traverse_single return meth(obj, **kw) File /home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/databases/sqlite.py, line 53, in visit_column self.recreate_table(table,column,delta) File /home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/databases/sqlite.py, line 36, in recreate_table self.execute() File /home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py, line 42, in execute return self.connection.execute(self.buffer.getvalue()) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1449, in execute params) File
Re: [galaxy-dev] nglims/removing multiplexing
On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman chapm...@50mail.com wrote: This was a typo in the downgrade function for one of the patches. I pushed a fix so if you update from bitbucket things should work smoothly again (once we get to problem 2 below). For anyone with galaxy-dist commit privileges, here's the one liner: https://bitbucket.org/chapmanb/galaxy-central/commits/463852762a6eeadcf177312330ad1cd01053263d Thanks Brad, added to stable branch in https://bitbucket.org/galaxy/galaxy-central/commits/0a06df7da177a204c7f3800ee39e5b9fd0956d7a ___ 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 database issue (?)
Hey Mo, The new volume we pushed out for the conference has several known issues. Enis and I are both away from the office on travel right now, but updating the volume and fixing these issues is the first thing I'll be doing when I'm back next week. For now, you can launch using the pre-conference AMI and cloudman bucket using something like https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop -Dannon On Tue, Jul 16, 2013 at 12:24 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hello, I found a couple of issues in using the latest version of Cloudman (revision:10201:ebe87051fadf). The Extract Genomic DNA tool returns an error: No sequences are available for 'mm9', request them by reporting this error. Upon trying to report the error in Galaxy (on the page that comes up when you click the bug icon) I get the error: Mail is not configured for this galaxy instance Any help on fixing the Extract Genomic DNA tool would be great. Thanks. Cheers, Mo Heydarian ___ 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] Cloudman master cannot connect to volume at start-up
Can you verify that the volume does still exist in your account, and that you're launching from the same availability zone that the volume exists in? On Mon, Jul 22, 2013 at 4:13 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: - This is what has been reported by the cluster status log: - - 20:01:14 - Master starting - 20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb: EC2ResponseError: 400 Bad Request**InvalidVolume.NotFound**The volume 'vol-91cfd1cb' does not exist. 9179663c-c5ec-4e90-88ff-ecf606b5e9a6 - 20:01:16 - Attempting to connect to a non-existent volume vol-91cfd1cb - 20:01:16 - Error processing filesystems in existing cluster configuration: 'NoneType' object has no attribute '__getitem__' - 20:01:16 - * Manager failed to start * Any suggestions? ___ 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] Cloudman - is it possible to still use depreciated AMIs ?
Yes, you can still use the deprecated AMIs. What error are you seeing when you try to ssh in? On Mon, Jul 22, 2013 at 4:30 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: I tried launching an instance specifying ami-da58aab3 as the AMI but I am unable to SSH or access Cloudman using the instance's URL. ___ 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] CloudMan Error
The warning message printed by the first ssh attempt indicates that you have no cloudman_key_pair.pem in the directory you executed the ssh command from. Find this file (or create a new one) and you'll be able to ssh. Good luck, and please keep threads on the list instead of emailing directly. Thanks! -Dannon On Mon, Jul 22, 2013 at 1:36 PM, deniz...@gmail.com wrote: Hi- the share string appears to be loading, but I am unable to ssh into my instance using the provided command, or anything like it. Instead I get the following: denizerezyilmaz$ ssh -i cloudman_key_pair.pem ubu...@ec2-54-242-61-164.compute-1.amazonaws.com Warning: Identity file cloudman_key_pair.pem not accessible: No such file or directory. OR: denizerezyilmaz$ ssh ec2-54-242-61-164.compute-1.amazonaws.com Permission denied (publickey). What am I missing? Thank you, Deniz ___ 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] All processes are freezed
The best contact address for these kinds of issues is galaxy-b...@bx.psu.edu . There was a brief delay with some jobs running, but everything should be working fine now. -Dannon On Wed, Jul 24, 2013 at 5:30 AM, Ali Sharifi Zarchi ashari...@gmail.comwrote: Hi everybody Since yesterday all processes I have run on Galaxy main are waiting. The system displayed a message to contact a Galaxy admin, but I could find no other way rather than this mailing list. Is this freeze due to a public maintenance, or it's just my problem? Best wishes, Ali ___ 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] CloudMan Error
On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz deniz...@gmail.comwrote: The workaround doesn't seem to work Can you tell me what happens when you launch with the workaround mentioned previously ( https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop)? This should launch the pre-migration AMI and Cloudman and shouldn't have any issues at all unless your cluster was already wonky. -Dannon ___ 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 Error
Ahh, ok, I misunderstood and thought you were saying there was a different error for the workaround. Are you able to send me the share string (directly if you want, feel free to drop the list) so that I might take a look? There should be no change at all in your instances from before the new release when using the workaround. On Fri, Jul 26, 2013 at 8:17 AM, Deniz Erezyilmaz deniz...@gmail.comwrote: Dannon- the problems that I saw were with the workaround (see last post). The instance launches, but the program stops when it can't find something (module/dependencies). There were also some different steps in setting up the instance. I had to create my own key pair, whereas in the past I never had to do that. I guess that simply using the share string that Greg at Janelia created made this step automatic. The cluster was working well at the end of June. The problem arose suddenly Saturday June 29, when the share string would not load. Thanks again, Deniz On Thu, Jul 25, 2013 at 5:19 PM, Dannon Baker dannon.ba...@gmail.comwrote: On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz deniz...@gmail.comwrote: The workaround doesn't seem to work Can you tell me what happens when you launch with the workaround mentioned previously ( https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop)? This should launch the pre-migration AMI and Cloudman and shouldn't have any issues at all unless your cluster was already wonky. -Dannon ___ 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] Problem with tabular files
What is the problem you're observing, and do you see any errors in the galaxy log or javascript console? -Dannon On Mon, Jul 29, 2013 at 5:51 AM, Misharl mon mish...@hotmail.com wrote: Hi everybody, In my lab, after upgrading our Galaxy instance to the latest version, we have a problem with displaying tabular files. Any idea from where the problem can come? Thanks in advance to all. Mish ___ 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] Problem with tabular files
What happens when you attempt view the tabular file? Does it automatically download instead of displaying, for example? On Mon, Jul 29, 2013 at 9:54 AM, Misharl mon mish...@hotmail.com wrote: Hi Dannon, Thank you very much for replying. The problem is that we cannot display any tabular files in the galaxy result panel. The tabular files are correct. We have checked the galaxy log, and didn't see anything. Thank you, Mish -- Date: Mon, 29 Jul 2013 07:57:28 -0400 Subject: Re: [galaxy-dev] Problem with tabular files From: dannon.ba...@gmail.com To: mish...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu What is the problem you're observing, and do you see any errors in the galaxy log or javascript console? -Dannon On Mon, Jul 29, 2013 at 5:51 AM, Misharl mon mish...@hotmail.com wrote: Hi everybody, In my lab, after upgrading our Galaxy instance to the latest version, we have a problem with displaying tabular files. Any idea from where the problem can come? Thanks in advance to all. Mish ___ 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] Cloudman - When will the symlinks be resolved ?
We're working on it but don't have a specific ETA for the release of the new volume. For now, you can continue to create and run non-migrated clusters using the previous version of Cloudman using this launch form: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop On Mon, Jul 29, 2013 at 10:49 AM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: I am referring to the following bug: https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt We are waiting for this bug to resolve before we fix any other issues with our Cloudman scripts. I am wondering when you think this bug will be resolved so I can plan my time. 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] CloudMan Error
Yes, I tried it and everything appeared to load fine using the url indicated above. The data volume was mounted correctly, and it appears the custom installation is in place though I would have no idea what it is or does. Did you install all the custom stuff originally? If not, it may be useful to talk to the person that did to find out if they're able to poke at it. That file that's indicated as missing (csamtools.so) is actually there if you take a look, and I'd expect it should all work if initialized correctly. On Tue, Jul 30, 2013 at 10:10 AM, Deniz Erezyilmaz deniz...@gmail.comwrote: HI - did you find anything with the share string? Thanks, Deniz On Fri, Jul 26, 2013 at 3:32 PM, Dannon Baker dannon.ba...@gmail.comwrote: Ahh, ok, I misunderstood and thought you were saying there was a different error for the workaround. Are you able to send me the share string (directly if you want, feel free to drop the list) so that I might take a look? There should be no change at all in your instances from before the new release when using the workaround. On Fri, Jul 26, 2013 at 8:17 AM, Deniz Erezyilmaz deniz...@gmail.comwrote: Dannon- the problems that I saw were with the workaround (see last post). The instance launches, but the program stops when it can't find something (module/dependencies). There were also some different steps in setting up the instance. I had to create my own key pair, whereas in the past I never had to do that. I guess that simply using the share string that Greg at Janelia created made this step automatic. The cluster was working well at the end of June. The problem arose suddenly Saturday June 29, when the share string would not load. Thanks again, Deniz On Thu, Jul 25, 2013 at 5:19 PM, Dannon Baker dannon.ba...@gmail.comwrote: On Thu, Jul 25, 2013 at 4:47 PM, Deniz Erezyilmaz deniz...@gmail.comwrote: The workaround doesn't seem to work Can you tell me what happens when you launch with the workaround mentioned previously ( https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop)? This should launch the pre-migration AMI and Cloudman and shouldn't have any issues at all unless your cluster was already wonky. -Dannon ___ 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] Error message
It shouldn't, unless the root cause of that error also affected the FTP transfer. Does FileZilla say there are any transmission errors? On Thu, Aug 1, 2013 at 1:16 AM, Mark Edward Fabreag merfabr...@gmail.comwrote: Good day! While I was uploading the file (through FileZilla), I encountered this message box: [image: Inline image 1] Will this affect uploading process? Thank you. ___ 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/ image.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/
Re: [galaxy-dev] Cloudman - When will the symlinks be resolved ?
The new volume update hasn't been released yet to fix those tool issues,
but the existing volume should actually appear in /mnt at launch.
On Thu, Aug 1, 2013 at 4:28 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote:
Thanks for letting me know, my old credentials have been disabled.
Anyways, that is all the log contained. I clicked on show all. Does
launching it with this method work on your end?
--
*From:* galaxy-dev-boun...@lists.bx.psu.edu [
galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Ravpreet Setia [
ravpreet.se...@oicr.on.ca]
*Sent:* Thursday, August 01, 2013 4:11 PM
*To:* Dannon Baker
*Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Cloudman - When will the symlinks be resolved
?
Here it is:
'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version: (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-01 20:07:40,138: Initializing app
[DEBUG] app:55 2013-08-01 20:07:40,138: Running on 'ec2' type of cloud.
[DEBUG] app:72 2013-08-01 20:07:40,138: Getting pd.yaml
[DEBUG] ec2:275 2013-08-01 20:07:40,138: No S3 Connection, creating a new one.
[DEBUG] ec2:278 2013-08-01 20:07:40,139: Got boto S3 connection.
[DEBUG] misc:113 2013-08-01 20:07:40,229: Checking if bucket
'cm-35f4d40b627583b6949bc5de11bcfecc' exists... it does not.
[DEBUG] misc:444 2013-08-01 20:07:40,229: Bucket
'cm-35f4d40b627583b6949bc5de11bcfecc' does not exist, did not get remote file
'persistent_data.yaml'
[INFO] app:78 2013-08-01 20:07:40,229: Master starting
[DEBUG] master:70 2013-08-01 20:07:40,229: Initializing console manager -
cluster start time: 2013-08-01 20:07:40.229549
[DEBUG] connection:648 2013-08-01 20:07:40,231: Start from server, version:
8.0, properties: {u'platform': 'Erlang/OTP', u'product': 'RabbitMQ',
u'version': '1.7.2', u'copyright': 'Copyright (C) 2007-2010 LShift Ltd.,
Cohesive Financial Technologies LLC., and Rabbit Technologies Ltd.',
u'information': 'Licensed under the MPL. See http://www.rabbitmq.com/'},
mechanisms: ['PLAIN', 'AMQPLAIN'], locales: ['en_US']
[DEBUG] connection:494 2013-08-01 20:07:40,263: Open OK! known_hosts
[ip-10-179-15-41.ec2.internal:5672]
[DEBUG] channel:70 2013-08-01 20:07:40,263: using channel_id: 1
[DEBUG] channel:484 2013-08-01 20:07:40,264: Channel open
[DEBUG] comm:35 2013-08-01 20:07:40,266: Successfully established AMQP
connection
[DEBUG] master:510 2013-08-01 20:07:40,266: Trying to discover any worker
instances associated with this cluster...
[DEBUG] ec2:246 2013-08-01 20:07:40,267: Establishing boto EC2 connection
[DEBUG] ec2:103 2013-08-01 20:07:40,267: Gathering instance zone, attempt 0
[DEBUG] ec2:108 2013-08-01 20:07:40,270: Instance zone is 'us-east-1d'
[DEBUG] ec2:263 2013-08-01 20:07:40,516: Got boto EC2 connection for region
'us-east-1'
[DEBUG] ec2:66 2013-08-01 20:07:40,574: Gathering instance id, attempt 0
[DEBUG] ec2:71 2013-08-01 20:07:40,575: Instance ID is 'i-7b386714'
[DEBUG] ec2:295 2013-08-01 20:07:40,639: Adding tag
'clusterName:gal_oldami_form2' to resource 'i-7b386714'
[DEBUG] ec2:295 2013-08-01 20:07:41,066: Adding tag 'role:master' to resource
'i-7b386714'
[DEBUG] master:174 2013-08-01 20:07:41,223: ud at manager start:
{'access_key': 'AKIAIUSCRANAJESP3GFQ', 'cloudman_home': '/mnt/cm',
'cluster_name': 'gal_oldami_form2', 'bucket_default': 'gxy-workshop',
'boot_script_name': 'cm_boot.py', 'bucket_cluster':
'cm-35f4d40b627583b6949bc5de11bcfecc', 'boot_script_path': '/tmp/cm', 'role':
'master', 'secret_key': 'EV12T4PMGSbM1IZmS7ZUJVi9nCvMncnrxXvytacJ',
'password': 'google'}
[DEBUG] pss:25 2013-08-01 20:07:41,224: Configured PSS as master
[DEBUG] master:204 2013-08-01 20:07:41,225: Cheking for and adding any
preconfigured services
[DEBUG] master:529 2013-08-01 20:07:41,225: Trying to discover any volumes
attached to this instance...
[DEBUG] base:55 2013-08-01 20:07:41,236: Enabling 'root' controller, class: CM
[DEBUG] buildapp:80 2013-08-01 20:07:41,239: Enabling 'httpexceptions'
middleware
[DEBUG] buildapp:86 2013-08-01 20:07:41,469: Enabling 'recursive' middleware
[DEBUG] buildapp:106 2013-08-01 20:07:41,719: Enabling 'print debug'
middleware
[DEBUG] buildapp:120 2013-08-01 20:07:41,734: Enabling 'error' middleware
[DEBUG] buildapp:130 2013-08-01 20:07:41,735: Enabling 'config' middleware
[DEBUG] buildapp:134 2013-08-01 20:07:41,736: Enabling 'x-forwarded-host'
middleware
[DEBUG] master:535 2013-08-01 20:07:41,737: Attached volumes:
[Volume:vol-fe5b7abe]
[INFO] master:198 2013-08-01 20:07:41,758: Completed initial cluster
configuration. This seems to be a new cluster; waiting to configure the type
[DEBUG] master:1627 2013-08-01 20:07:41,758: Monitor started; manager started
Starting server in PID 1252.
serving on 0.0.0.0:42284 view at http://127.0.0.1:42284
[DEBUG] master:1247 2013-08-01 20
Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer
Hi Boaz, You should be able to edit universe_wsgi.ini (line ~30) to specify any port you'd like -- so simply pick something other than 8080, save the file, and retry. Remember to remove the hash (#) at the beginning of the line to have it take effect. -Dannon On Mon, Aug 5, 2013 at 12:42 PM, Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, I think I'm running into a problem of getting my local galaxy installation server to start because another httpd server is currently running on the same computer (see attached output of run.sh). Toward the end of the attached file you'll notice that the server starts with PID number but then runs into a socket conflict (probably with the other server) and stops. Is there a way to get over this problem? Or am I wrong in my diagnosis? I did manage to get the galaxy server to start about 2 weeks ago while no other httpd server was running. I then switched the galaxy server off and now I run into this problem while trying to restart it. Thanks for your help. Boaz *Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710* ** ** * * ___ 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] Galaxy on cloud config issues
A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly ulyanov_anat...@allergan.com wrote: Hello, ** ** Does anybody use the last Galaxy image? I am running Galaxy image on EC2:* *** ** ** Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 ** ** It looks as those three tools have configuration problems: ** ** EBOSS Blast+ meme ** ** For all three I am getting a message that looks like that: ** ** /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp ** ** Is there a way to fix configuration files for those tools? ** ** Thank you. ** ** Best Regards, Anatoly ** ** This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___ 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] Galaxy on cloud config issues
Ravpreet -- can you provide details as to what's failing for you? If I remember correctly, you had an odd issue where nothing was actually appearing at /mnt, right? This will not be the same issue as the tool volume update. On Thu, Aug 8, 2013 at 4:36 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: Anatoly, did this method work for you? It is not working for me. -- *From:* galaxy-dev-boun...@lists.bx.psu.edu [ galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Dannon Baker [ dannon.ba...@gmail.com] *Sent:* Wednesday, August 07, 2013 8:00 PM *To:* Ulyanov_Anatoly *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Galaxy on cloud config issues A new tools volume will be released shortly. For now, you can launch the previous cloudman release using the following: https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly ulyanov_anat...@allergan.com wrote: Hello, ** ** Does anybody use the last Galaxy image? I am running Galaxy image on EC2: ** ** Instance ID i-1b2d3773 Image ID (AMI) ami-118bfc78 ** ** It looks as those three tools have configuration problems: ** ** EBOSS Blast+ meme ** ** For all three I am getting a message that looks like that: ** ** /mnt/galaxy/tmp/job_working_directory/000/2/galaxy_2.sh: blastp: not found Error invoking command: blastp ** ** Is there a way to fix configuration files for those tools? ** ** Thank you. ** ** Best Regards, Anatoly ** ** This e-mail, including any attachments, is meant only for the intended recipient and may be a confidential communication or a communication privileged by law. If you received this e-mail in error, any review, use, dissemination, distribution, or copying of this e-mail is strictly prohibited. Please notify the sender immediately of the error by return e-mail and please delete this message from your system. Thank you in advance for your cooperation. ___ 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] Galaxy on cloud config issues
On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: Yeah, nothing happens after SGE gets to the running state. The directory structure of the old ami does not appear in /mnt. The log was posted in the following thread: Ahh, ok - I assumed since there was no further reply that the workaround worked for you. I'll take another look at your log, but if you could follow up (on that other thread) with some more details about your cluster that'd be great. Specifically, how you're launching it, if it's an old cluster being relaunched, a share_string-based new cluster, etc. Additionally, I am not sure what you mean by, This will not be the same issue as the tool volume update.. If your volume isn't even mounting, then it has nothing to do with the symlinks referred to by Ulyanov. His volume mounts, it's just not completely functional. ___ 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] Error at initialization of module heapycTraceback / Last sources of Galaxy
This looks to be a guppy bug that has now been fixed ( http://sourceforge.net/p/guppy-pe/bugs/10/) so we'll update the egg from our end, thanks! For now, you can either build your own guppy 0.1.9+ egg to fix it or disable use_memdump in your universe (to skip it completely). Unless you're actually using the memdump capabilities, I'd recommend having it off for performance reasons anyway. -Dannon On Mon, Aug 12, 2013 at 7:56 AM, Sarah Maman sarah.ma...@toulouse.inra.frwrote: Dear all, When I try to install last sources of Galaxy(% hg clone https://bitbucket.org/galaxy/**galaxy-dist/https://bitbucket.org/galaxy/galaxy-dist/) , I have this error : Error at initialization of module heapycTraceback (most recent call last): File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/lib/** galaxy/webapps/galaxy/**buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/lib/**galaxy/app.py, line 157, in __init__ self.memdump = memdump.Memdump() File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/lib/**galaxy/util/memdump.py, line 24, in __init__ self.heapy = guppy.hpy() File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/__init__.py**, line 35, in hpy return r.guppy.heapy.Use File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 44, in __getattr__ return self._share.getattr(self, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 187, in getattr d = self.getattr2(inter, cache, owner, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 202, in getattr2 x = self.getattr_package(inter, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 250, in getattr_package x = self.makeModule(x, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 310, in makeModule return Share(module, self, module.__name__, Clamp) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 176, in __init__ getattr(inter, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 44, in __getattr__ return self._share.getattr(self, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 187, in getattr d = self.getattr2(inter, cache, owner, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 204, in getattr2 x = self.getattr3(inter, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 272, in getattr3 pa = getattr(pa, at) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 44, in __getattr__ return self._share.getattr(self, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 187, in getattr d = self.getattr2(inter, cache, owner, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 202, in getattr2 x = self.getattr_package(inter, name) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/etc/Glue.py**, line 239, in getattr_package x = __import__(self.makeName(name)**, globals(), locals()) File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/heapy/View.**py, line 556, in module prime_builtin_types() File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/heapy/View.**py, line 539, in prime_builtin_types import guppy.heapy.heapyc File /usr/local/bioinfo/src/**galaxy-dev/galaxy-dist/eggs/** guppy-0.1.8-py2.7-linux-x86_**64-ucs2.egg/guppy/sets/__init_**_.py, line 3, in module from setsc import BitSet# base bitset type ImportError: /usr/local/bioinfo/src/galaxy-**dev/galaxy-dist/eggs/guppy-0. **1.8-py2.7-linux-x86_64-ucs2.**egg/guppy/sets/setsc.so: undefined symbol: _PyLong_AsScaledDouble Coul you please help me ? Thanks in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de
Re: [galaxy-dev] Workflow action summary confusing, repeats Hide this dataset
Peter,
Thanks for noticing this -- the text in the UI should definitely reflect
which output it's referring to. Hide output_pos, etc.
https://trello.com/c/KAtwLSiV/1069-workflow-actions-cosmetic-issues
-Dannon
On Wed, Aug 21, 2013 at 7:16 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Hi all,
I have found two potential bugs with how workflow actions are
described to the user when running a workflow.
I am looking over the run workflow dialogue for this workflow,
(I currently get a warning due to the filter tool having a new
Number of header lines to skip option)
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
I manually imported the *.ga file due to issues with the Tool Shed
workflow import,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016209.html
I am running the latest galaxy-dist,
$ sudo -u galaxy hg head
changeset: 10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
changeset: 10408:6822f41bc9bb
branch: stable
parent: 10393:d05bf67aefa6
user:Dave Bouvier d...@bx.psu.edu
date:Mon Aug 19 13:06:17 2013 -0400
summary: Fix for case where running functional tests might
overwrite certain files in database/files.
--
For step 2, the details view says:
Actions:
Hide this dataset.
Hide this dataset.
I find that confusing, and initially thought there might be a
bug or duplicated action. Actually it is just a misleading
summary as this tool can produce TWO outputs:
post_job_actions: {
HideDatasetActionoutput_neg: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_neg
},
HideDatasetActionoutput_pos: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_pos
}
},
Perhaps the Hide this dataset message could be less
ambiguous by using the output variable names (as in
some of the other action descriptions)?
There are similar problems with the next steps too.
--
Steps 6 and 7 are also odd. For step 6 the details view says:
Actions:
Hide this dataset.
Rename output 'out_file1' to 'Filtered SignalP results'.
Hide this dataset.
Rename output 'out_file1' to 'Filtered SignalP results'.
Likewise for step 7,
Actions:
Hide this dataset.
Rename output 'output_pos' to 'Secreted proteins'.
Hide this dataset.
Rename output 'output_pos' to 'Secreted proteins'.
Again, there seems to be a duplication of the messages.
It should be hiding one output, and renaming the other, e.g.
post_job_actions: {
HideDatasetActionoutput_neg: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_neg
},
RenameDatasetActionoutput_pos: {
action_arguments: {
newname: Secreted proteins
},
action_type: RenameDatasetAction,
output_name: output_pos
}
},
--
In some ways this is just a harmless cosmetic issue, but
it does seem confusing to me.
Thanks,
Peter
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Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Hey Peter, I've reproduced this here, thanks. Unfortunately this got missed previously, once we had the import itself working. To be clear, though, the workflow itself is still completely functional, imports and runs, and the only issue is the inability to view the svg? I think what's causing this is that generate_workflow_image uses completely separate workflow modules which didn't have my previous fixes applied. This should be refactored so we don't have duplicated code sitting around, but I'll go ahead and patch it to get it working again shortly. On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hi Dannon, I'm seeing a problem which seems very similar to the one Bjoern had back in June with the same workflow (which appeared to have been fixed according to the old IUC thread Workflow import is not working). This server is running the current galaxy-dist release, $ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user:Dave Bouvier d...@bx.psu.edu date:Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files. I have just installed this workflow repository with its dependencies (some of where I had previously installed via the Tool Shed). Most of the tools were actually already manually installed but have been commented out in my tool_conf.xml file: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 Installation appeared to be successful, so I wanted to import the workflow into Galaxy. I clicked on the workflow and expected to see an SVG of the workflow and the import action to be available. In the browser I saw: quote Find secreted proteins with TMHMM and SignalP (this page displays SVG graphics) Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. /quote On the terminal I have: 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] GET /galaxy/admin_toolshed/browse_repositories HTTP/1.1 200 - http://ppcollab/galaxy/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falseoperation=manage_repositoryid=eede92f8a72bf85df-deleted=False HTTP/1.1 302 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] GET /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] GET /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 500 - http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 Error - type 'exceptions.KeyError': 'header_lines' URL: http://ppcollab/galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Quick followup on this one -- had you manually tweaked this workflow prior to upload? I see all of the tool identifiers are the short form 'signalp3' and not the long-form toolshed included versions. On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker dannon.ba...@gmail.comwrote: Hey Peter, I've reproduced this here, thanks. Unfortunately this got missed previously, once we had the import itself working. To be clear, though, the workflow itself is still completely functional, imports and runs, and the only issue is the inability to view the svg? I think what's causing this is that generate_workflow_image uses completely separate workflow modules which didn't have my previous fixes applied. This should be refactored so we don't have duplicated code sitting around, but I'll go ahead and patch it to get it working again shortly. On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hi Dannon, I'm seeing a problem which seems very similar to the one Bjoern had back in June with the same workflow (which appeared to have been fixed according to the old IUC thread Workflow import is not working). This server is running the current galaxy-dist release, $ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user:Dave Bouvier d...@bx.psu.edu date:Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files. I have just installed this workflow repository with its dependencies (some of where I had previously installed via the Tool Shed). Most of the tools were actually already manually installed but have been commented out in my tool_conf.xml file: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 Installation appeared to be successful, so I wanted to import the workflow into Galaxy. I clicked on the workflow and expected to see an SVG of the workflow and the import action to be available. In the browser I saw: quote Find secreted proteins with TMHMM and SignalP (this page displays SVG graphics) Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. /quote On the terminal I have: 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] GET /galaxy/admin_toolshed/browse_repositories HTTP/1.1 200 - http://ppcollab/galaxy/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falseoperation=manage_repositoryid=eede92f8a72bf85df-deleted=False HTTP/1.1 302 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] GET /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] GET /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 500 - http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 Error - type 'exceptions.KeyError': 'header_lines' URL: http://ppcollab/galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? Yep, that's where it was. These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :) ___ 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] Workflow import is not working, KeyError: 'header_lines'
Hey Peter, The reason it's actually failing has to do with the tool Filter1, and your particular version of the filter tool not having the header lines parameter. This was added in 8678:a14006775b08. In this instance, we should have just used the default value. Once all tools and versions are in the toolshed, this sort of thing shouldn't crop up because you'll have the correct version available. I've committed a temporary fix in 10423:3c60f6a7dedc. On Wed, Aug 21, 2013 at 9:14 AM, Dannon Baker dannon.ba...@gmail.comwrote: On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? Yep, that's where it was. These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :) ___ 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] Galaxy in the cloud.... some questions
Hi Alistair, One major goal of the Galaxy cloud offering is that it works out of the box with a very large selection of tools and indices installed and ready to go, with no configuration necessary. My workshop heuristic is two students per node using regular m1.xlarge nodes (though input from others on this is absolutely welcome!). For costs, see http://aws.amazon.com/ec2/#pricingfor detailed pricing information, but for the most part what you need to know is: You'll need a head node up for the entire lifespan of your cluster. You can terminate this and start it back up (and avoid paying for the node use in the interim), but any time you want to interact with this cluster it will need to be alive. We generally use a high memory quadruple extra large instance @ ~1.65/hr. I'd start with this, and start with *more* space on the galaxy volume than you think you'll need -- space is not expensive, especially if you're not keeping it for more than a few days to cover a workshop. Worker nodes will be the brunt of your costs, and fortunately these are *trivial* to add and remove and can be configured just prior to and after the workshop. if you use standard m1.xlarge instances, they're ~.48/hour. So, for 10 of them to cover your 20 students, you're looking at about $5/hour for the workshop -- not too bad. Amazon will bill you for every hour you have an instance, regardless of whether you're using it or not. Do make sure to terminate things when you're done and/or not utilizing it anymore. You may want to look into Cloudman's auto-scaling to handle this for you -- this allows you to say something like Keep 2 worker instances up all the time, but under heavy use scale up to at most 10. I wouldn't recommend auto-scaling for a workshop, however, I'd have the instances ready ahead of time since you're fairly certain you'll need them. Regarding setting up ahead of time, what I'd recommend is to set up just the master instance (which you will pay for) ahead of time, test it out, and only add the workers when it's time to kick off the workshop. One more performance tip is that for workshops, once you've added extra worker nodes, you'll want to go into the Cloudman admin panel and disable job running on the master node (just a single button click) for maximum performance of the galaxy application. We're in the middle of an update that will be released early next week (already accessible using the cloudman-dev bucket), which fixes several known issues with the current tool offering, so if you're able I'd wait until that happens before starting a new workshop cluster that's probably for the best. Additionally, we have a supported 'workshop-ready' offering that has preloaded data for our Galaxy101 and RNA-seq exercises, among other things. This will be updated with our forthcoming release, but see http://wiki.galaxyproject.org/Teach/WorkshopAMI for more details. Good luck, and let me know if there's anything else I can do to help out! Dannon On Thu, Aug 22, 2013 at 9:45 PM, Alistair Chilcott alistair.chilc...@utas.edu.au wrote: Hi, ** ** Firstly this is my first post to the list so be gentle :D ** ** We have been looking at the Galaxy in the Cloud option for our researchers ** ** We have been doing a fair bit of reading on the various source but haven’t found any solid answers to the following questions: ** ** -When it is started (AWS account setup and launched from the “new cloud cluster link”) how much config is required to get it running all the tools such as megablast, Bowtie, Tophat etc? (We have also been setting up a local install of Galaxy but are struggling with the setup of these tools that don’t come bundled with the base Galaxy install) ** ** -What size AWS cluster would be required to support a class of 20 or so students running a range of relatively short tasks with Megablast, Bowtie, Tophat, Fastq Groomer, SAM tools? ** ** -how is the AWS charge calculated does it run while the cluster is available or just for the actual compute time used? Ie Could setup it up and have it ready but while it isn’t processing data it’s not costing anything? ** ** Regards, ** ** Alistair ** ** [image: Description: Description: Description: Description: Description: Description: cid:image001.png@01CA36CF.30513900] *Alistair Chilcott* Systems Administrator, (Domain) Information Technology Services Email: alistair.chilc...@utas.edu.au | P: +61 3 6226 7743 University of Tasmania, Locked Bag 23, Hobart Tas. 7000 ** ** ** ** ___ 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:
Re: [galaxy-dev] Postgresql database cleaning
Can you get a dump of table sizes for us to compare with? http://wiki.postgresql.org/wiki/Disk_Usage On Thu, Aug 29, 2013 at 12:05 PM, Nate Coraor n...@bx.psu.edu wrote: On Aug 29, 2013, at 11:50 AM, Nate Coraor wrote: On Aug 26, 2013, at 5:03 AM, Christophe Antoniewski wrote: Hi everybody, The python scripts to clean histories, datasets, users etc.. are fine... However, the records are not really removed from the postgresql database and as a result, this one gets bigger and bigger with unused records. Ours is above 1 To after 2 years of production. Is there a safe way to clean the database from unused records and their dependencies to reduce it size, without being a postgresql guru ? Hi Chris, The database maintains a permanent record of everything that was done, even though the underlying data can be removed. There are a lot of dependencies between objects in Galaxy and removing records, especially anything with a foreign key, could easily result in a lot of problems with all kinds of things, from the UI to running jobs. Because of this, records cannot be removed from the database. Somehow I missed that you said your database is 1 TB - that should not be the case. Unless your database is not being vacuumed or you create objects at an extreme rate, it seems as though something has been stored in it that should not have. --nate --nate Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.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/ 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/ ___ 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] iRODS integration
The iRods integration is under active development, follow progress here: https://trello.com/c/Sp9XvRfD/1072-object-store-write-an-irods-plugin. -Dannon On Thu, Sep 5, 2013 at 11:27 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi All, Is there any update on iRods integration in galaxy ? One major concern presented in deployment of Galaxy is that all of the researcher data is access by a user id (linux) running galaxy server. This is typical webserver problem. May be it is some how resolved by iRods or any other better Authn based FS. any suggestion ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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] iRODS integration
That's weird, the board is public. Are you able to go to the root development board? https://trello.com/b/75c1kASa On Thu, Sep 5, 2013 at 11:32 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Dannon, i could not get access to that trello page. can you kindly invite me ? zas...@pdc.kth.se On Thu, Sep 5, 2013 at 5:31 PM, Dannon Baker dannon.ba...@gmail.comwrote: The iRods integration is under active development, follow progress here: https://trello.com/c/Sp9XvRfD/1072-object-store-write-an-irods-plugin. -Dannon On Thu, Sep 5, 2013 at 11:27 AM, Zeeshan Ali Shah zas...@pdc.kth.sewrote: Hi All, Is there any update on iRods integration in galaxy ? One major concern presented in deployment of Galaxy is that all of the researcher data is access by a user id (linux) running galaxy server. This is typical webserver problem. May be it is some how resolved by iRods or any other better Authn based FS. any suggestion ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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/ -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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] pgcleanup problem
Eric, What version of posgresql are you using? The script has a comment that indicates you need 9.1+ (and I'm using 9.1.9), and it works out of the box for me. -Dannon On Fri, Sep 20, 2013 at 7:35 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hi All, I'm trying to do some cleanup in my test environment (galaxy-dist) and pgcleanup.py ends with Traceback (most recent call last): File ./scripts/cleanup_datasets/pgcleanup.py, line 773, in module cleanup = Cleanup() File ./scripts/cleanup_datasets/pgcleanup.py, line 55, in __init__ self.__connect_db() File ./scripts/cleanup_datasets/pgcleanup.py, line 114, in __connect_db self.conn = psycopg2.connect(**args) TypeError: 'username' is an invalid keyword argument for this function Unless I add args['user'] = args['username'] del args['username'] Is this a bug or a config error? Eric ___ 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] Local Galaxy Install - Multiple Input Files for Workflow Missing?
Are you using Input Dataset steps in your workflows? The multiple inputs feature uses these to know how to distribute inputs -- other than that no other configuration steps are necessary. On Tue, Sep 24, 2013 at 2:43 PM, Adam Brenner aebre...@uci.edu wrote: Howdy, On our local galaxy cluster, I have gotten a report that the multiple input files selection on workflows is missing. How do I enable it? Looking at the past mailing list[1] this is the item that is missing from our setup -- the tooltip icon. We are running a version of galaxy that is roughly ~one month old: c42567f43aa7. [1]: http://dev.list.galaxyproject.org/Looking-for-recommendations-How-to-run-galaxy-workflows-in-batch-td4362836.html#a4362874 Thanks! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.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/ 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] Galaxy STARTUP ERROR!
This looks to be a bug with the version of babel we're using (fixed in a
newer revision that I'll update to after testing), combined with improperly
set environment variables. Can you check your environment (just `env` in a
terminal) and look for LC_ALL, LANGUAGE, and LANG. Are any of these set to
*just* utf-8? It looks like they should probably be in a format like
en_US.utf-8.
On Wed, Oct 2, 2013 at 5:30 AM, Giovanni Pascarella muju...@hotmail.comwrote:
Hi!
I am trying to launch Galaxy locally but I'm getting the following error:
*tkx417:galaxy pascarellagiovanni$ sh run.sh*
*Traceback (most recent call last):*
* File ./scripts/paster.py, line 33, in module*
*serve.run()*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 1049, in run*
*invoke(command, command_name, options, args[1:])*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke*
*exit_code = runner.run(args)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 220, in run*
*result = self.command()*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 643, in command*
*app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp*
*return loadobj(APP, uri, name=name, **kw)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 374, in loadobj*
*global_conf=global_conf)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 399, in loadcontext*
*global_conf=global_conf)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 423, in _loadconfig*
*return loader.get_context(object_type, name, global_conf)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 561, in get_context*
*section)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 620, in _context_from_explicit*
*value = import_string(found_expr)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 125, in import_string*
*return pkg_resources.EntryPoint.parse(x= + s).load(False)*
* File /Users/pascarellagiovanni/Desktop/galaxy/lib/pkg_resources.py,
line 1954, in load*
*entry = __import__(self.module_name, globals(),globals(),
['__name__'])*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/__init__.py, line
4, in module*
*from framework import expose*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/framework/__init__.py,
line 40, in module*
*from babel.support import Translations*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/support.py,
line 29, in module*
*from babel.dates import format_date, format_datetime, format_time,
LC_TIME*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py,
line 34, in module*
*LC_TIME = default_locale('LC_TIME')*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 642, in default_locale*
*return '_'.join(filter(None, parse_locale(locale)))*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 763, in parse_locale*
*raise ValueError('expected only letters, got %r' % lang)*
*ValueError: expected only letters, got 'utf-8'*
Anybody knows what this is about?
Thanks,
Giovanni
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Re: [galaxy-dev] GA file format documentation
Nothing formal. The .ga extension is simply the workflow dictionary exported as .json, if that helps -- there's no extra magic to the format. You may want to look at the workflow API, some users have had success integrating workflows created on the fly using it. -Dannon On Mon, Oct 7, 2013 at 11:19 AM, Philip Mabon philipma...@gmail.com wrote: Is there any documentation on how exported workflow with '.ga' extension are structured? We are looking for the ability to create our workflows without using the workflow editor thru the web portal. Thanks Takadonet ___ 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] GA file format documentation
Right, so you'd assemble the json clientside and use /api/workflows/upload to create it. See the import_new_workflow method for more details On Mon, Oct 7, 2013 at 12:31 PM, Philip Mabon philipma...@gmail.com wrote: API allows for importing and exporting of workflows but nothing for creating a new workflow. I will dig and see if anyone has published or presented on their internal libraries that create workflows on the fly. Thanks Takadonet On Mon, Oct 7, 2013 at 11:18 AM, Dannon Baker dannon.ba...@gmail.comwrote: Nothing formal. The .ga extension is simply the workflow dictionary exported as .json, if that helps -- there's no extra magic to the format. You may want to look at the workflow API, some users have had success integrating workflows created on the fly using it. -Dannon On Mon, Oct 7, 2013 at 11:19 AM, Philip Mabon philipma...@gmail.comwrote: Is there any documentation on how exported workflow with '.ga' extension are structured? We are looking for the ability to create our workflows without using the workflow editor thru the web portal. Thanks Takadonet ___ 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] Launching CloudMan in Other AWS Regions than US East
On Tue, Oct 8, 2013 at 4:48 AM, Ryota Yamanaka yaman...@genome.rcast.u-tokyo.ac.jp wrote: 1) Do you plan to clone CloudMan AMI to other regions outside the US in the near future? 2) Or, is there any way we can build CloudMan in such regions, with or without your support? Yes, we do plan on addressing this in the near term; it's something we've actually been discussing this past week. The plan is for galaxy to be mirrored in each region, and we hope to have more details soon. You *could* build it yourself, but it's an involved process and depending on the timeframe for your project it might be best to wait. Let me know if you'd like more details. ___ 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] cloning Galaxy cluster on cloud Amazon EC2
Whoever your organization administrator is will need to either create those keys for you, or allow your IAM user access to them. Are you able to contact the person that administers your account? On Tue, Oct 29, 2013 at 10:52 AM, Manisha Sapre msa...@nmdp.org wrote: Good Morning Dannon we have paid amazon service, I log into EC2 using organization credentials, but get that screen ( below) while trying to identify account text string in AWS console section Launching a cloud instance of galaxy would require this account text string ___ 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] cloning Galaxy cluster on cloud Amazon EC2
Maybe I misunderstand what you're trying to do, but you shouldn't have to use ssh-add or anything of the sort; cloudlaunch will do this for you. When you put your credentials into those two boxes at usegalaxy.org/cloudlaunch, what exactly happens? On Tue, Oct 29, 2013 at 11:21 AM, Manisha Sapre msa...@nmdp.org wrote: Yes , all users have been allotted a private key , this error is after ssh-add ( private key), From: Dannon Baker dannon.ba...@gmail.com Date: Tuesday, October 29, 2013 10:15 AM To: System Administrator msa...@nmdp.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu, David Roe d...@nmdp.org Subject: Re: [galaxy-dev] cloning Galaxy cluster on cloud Amazon EC2 Whoever your organization administrator is will need to either create those keys for you, or allow your IAM user access to them. Are you able to contact the person that administers your account? On Tue, Oct 29, 2013 at 10:52 AM, Manisha Sapre msa...@nmdp.org wrote: Good Morning Dannon we have paid amazon service, I log into EC2 using organization credentials, but get that screen ( below) while trying to identify account text string in AWS console section Launching a cloud instance of galaxy would require this account text string ___ 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] cloning Galaxy cluster on cloud Amazon EC2
Your ssh keys are completely different from the keys you're looking for here. An AWS account with root access should be able to see these, as far as I know, but since you're unable to see them for whatever reason you will need to contact the primary administrator for your AWS account and I'm sure they can help you out. On Tue, Oct 29, 2013 at 11:30 AM, Manisha Sapre msa...@nmdp.org wrote: I am unable to put any credentials into those boxes , as I don't see the account text string in AWS console( permission denied screen), hence I tried adding it manually using ssh-add Should this be a problem with root access ? Thanks From: Dannon Baker dannon.ba...@gmail.com Date: Tuesday, October 29, 2013 10:25 AM To: System Administrator msa...@nmdp.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu, David Roe d...@nmdp.org Subject: Re: [galaxy-dev] cloning Galaxy cluster on cloud Amazon EC2 Maybe I misunderstand what you're trying to do, but you shouldn't have to use ssh-add or anything of the sort; cloudlaunch will do this for you. When you put your credentials into those two boxes at usegalaxy.org/cloudlaunch, what exactly happens? On Tue, Oct 29, 2013 at 11:21 AM, Manisha Sapre msa...@nmdp.org wrote: Yes , all users have been allotted a private key , this error is after ssh-add ( private key), From: Dannon Baker dannon.ba...@gmail.com Date: Tuesday, October 29, 2013 10:15 AM To: System Administrator msa...@nmdp.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu, David Roe d...@nmdp.org Subject: Re: [galaxy-dev] cloning Galaxy cluster on cloud Amazon EC2 Whoever your organization administrator is will need to either create those keys for you, or allow your IAM user access to them. Are you able to contact the person that administers your account? On Tue, Oct 29, 2013 at 10:52 AM, Manisha Sapre msa...@nmdp.org wrote: Good Morning Dannon we have paid amazon service, I log into EC2 using organization credentials, but get that screen ( below) while trying to identify account text string in AWS console section Launching a cloud instance of galaxy would require this account text string ___ 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] Supporting file sets for running a tool with multiple input files
Hi Pieter, We've worked out what we think is the right way to solve this for Galaxy and expect work to start soon. See the trello card ( https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more details. For your particular tool, the first workaround that comes to mind would be adding a new datatype, say, ZippedInputFiles in your toolshed repository that gets included and used by users, though I haven't actually tried that. That said, I'd probably wait, this feature is high on our list of things to do next. -Dannon On Mon, Nov 4, 2013 at 5:44 AM, Lukasse, Pieter pieter.luka...@wur.nlwrote: Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl ___ 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] Write all intermediate workflow data to /tmp/ only
A short term option that just occurred to me would be to run a sort of post-job-action for output datasets, deleting any non-output non-necessary (anymore) intermediate parents. On Wed, Nov 13, 2013 at 11:59 AM, John Chilton chil...@msi.umn.edu wrote: On Wed, Nov 13, 2013 at 10:34 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Nov 12, 2013 at 7:13 PM, Ben Gift corn8b...@gmail.com wrote: I'm working with a lot of data on a cluster (condor). If I save all the workflow intermediate data, as Galaxy does by default (and rightfully so), it fills the drives. How can tell Galaxy to use /tmp/ to store all intermediate data in a workflow, and keep the result? You can't - for a start /tmp is usually machine specific so the /tmp used by one cluster node is probably not going to be available on the /tmp of the other cluster nodes, and different stages of the workflow are likely to be run on different cluster nodes. I imagine I'll have to work on how Galaxy handles jobs, but I'm hoping there is something built in for this. Workflows can mark the output datasets, and the rest are automatically hidden/deleted on successful completion (but kept and visible on request via the history menu). It might be nice if we could make that more aggressive and actually purge the intermediate files from disk as well? Ability to have these deleted is not available, but it should be an option. Here is the most relevant Trello card. https://trello.com/c/YfLGkJKe Even this small step will probably require tracking some concept of a running workflow in the database or a message queue, I don't think this is being done currently but I think Dannon is working on the queue piece. Once that is in place, there are still many things that could be done better in arena. Nate has mentioned building functionality into object stores and job planning so that data could be pre-staged where it needs to be ahead of time in a workflow. Along similar lines, one could also imagine implementing/configuring an object store that simply wrote files that are pre-marked for deletion (once implemented) to faster staging/scratch disk on the cluster. Having this advanced planning logic built in are probably prerequistes to allowing the use of named pipes or in memory data files some day. A lot of things to work on and there is a long way to go. I have created a Trello card for this and will link to this thread. But it should probably be spelled out more concretely and broken into multiple cards. https://trello.com/c/dUMOHHmM -John 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/ 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/ ___ 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] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November
This may be due to an incorrect reference to '/mnt/galaxyTools' in the galaxy user's .sge_request file. If you're comfortable with ssh and editing files on the server, you can log in and edit the file (the path should be /mnt/galaxy instead), and you should be good to go. Feel free to reply offline if you're not comfortable with this and would like me to take a look directly. On Mon, Nov 18, 2013 at 8:41 AM, Young, Lynn (NIH/OD/ORS) [E] ly...@mail.nih.gov wrote: Hi, We're using Galaxy Cloud - New Cloud Cluster to create instances of Galaxy for training on Wednesday 20 November. When we try to view a bam file using Trackster, we get the following error: /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedtools: command not found /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedGraphToBigWig: command not found Please let us know how to proceed. Sincerely, Lynn Lynn Young, PhD | Informationist/Bioinformatics Scientist | National Institutes of Health Library | Office of Research Services | Building 10, Room B1L-306D | 10 Center Drive | Bethesda, Maryland 20892-1150 | T. 301-594-6426 | F. 301-402-0254 | E. ly...@mail.nih.govmailto: ly...@mail.nih.gov | http://twitter.com/bioinformatics1 Stay connected with the NIH Library NIH Library: http://nihlibrary.nih.govhttp://nihlibrary.nih.gov/ | Facebook: http://www.facebook.com/nihlibrary | Twitter: http://www.twitter.com/nihlibhttp://www.twitter.com/nihlib _ Amazing Research. Amazing Help. ___ 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] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November
I believe subsequent jobs should use the new paths automatically, yes. On Mon, Nov 18, 2013 at 12:14 PM, Young, Lynn (NIH/OD/ORS) [E] ly...@mail.nih.gov wrote: Hi Dannon, I edited the file. Will the system automatically recognize the change? Warmly, Lynn From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com Date: Monday, November 18, 2013 1:06 PM To: Lynn Young ly...@mail.nih.govmailto:ly...@mail.nih.gov Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] ACTION needed: fix error in Cloud Cluster Galaxy Trackster DATE needed: needed for workshop on Wednesday 20 November This may be due to an incorrect reference to '/mnt/galaxyTools' in the galaxy user's .sge_request file. If you're comfortable with ssh and editing files on the server, you can log in and edit the file (the path should be /mnt/galaxy instead), and you should be good to go. Feel free to reply offline if you're not comfortable with this and would like me to take a look directly. On Mon, Nov 18, 2013 at 8:41 AM, Young, Lynn (NIH/OD/ORS) [E] ly...@mail.nih.govmailto:ly...@mail.nih.gov wrote: Hi, We're using Galaxy Cloud - New Cloud Cluster to create instances of Galaxy for training on Wednesday 20 November. When we try to view a bam file using Trackster, we get the following error: /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedtools: command not found /opt/sge/default/spool/execd/ip-10-32-111-66/job_scripts/14: line 13: bedGraphToBigWig: command not found Please let us know how to proceed. Sincerely, Lynn Lynn Young, PhD | Informationist/Bioinformatics Scientist | National Institutes of Health Library | Office of Research Services | Building 10, Room B1L-306D | 10 Center Drive | Bethesda, Maryland 20892-1150 | T. 301-594-6426 | F. 301-402-0254 | E. ly...@mail.nih.govmailto: ly...@mail.nih.govmailto:ly...@mail.nih.govmailto:ly...@mail.nih.gov | http://twitter.com/bioinformatics1 Stay connected with the NIH Library NIH Library: http://nihlibrary.nih.govhttp://nihlibrary.nih.gov/ | Facebook: http://www.facebook.com/nihlibrary | Twitter: http://www.twitter.com/nihlibhttp://www.twitter.com/nihlib _ Amazing Research. Amazing Help. ___ 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] unable to share dataset history
Hi, That sort of sharing only works within a single galaxy instance; users are not shared between different galaxies. To copy an entire history from one instance to another you will want to use the history export/import functionality. History context menu - Export to file on the source instance, and Import from file on the destination. -Dannon On Tue, Nov 19, 2013 at 11:20 AM, Manisha Sapre msa...@nmdp.org wrote: Hello Team Galaxy trying to share/ forward dataset history from user 1 ( running on a local instance,Scrn.1) to user 2 (running on cloud amazon ec2 instance,Scrn.2) and *vice-versa*, error:- user is not a valid galaxy user. getting this error while both the users are logged into system and both the instance's are running normal. insights of team will be very helpful. Thanks msapre ___ 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] unable to share dataset history
Data transfer into Amazon's cloud is completely free. Data out is what costs money. See http://aws.amazon.com/pricing_effective_july_2011/ What you're trying to do here would be loading data *into* amazon from our main server at usegalaxy.org. I'm not sure what you're asking with the second question there -- in a cloud instance the master and worker nodes are all inside the cloud, and communication between them is both free, and very fast. -Dannon On Wed, Nov 20, 2013 at 8:43 AM, Manisha Sapre msa...@nmdp.org wrote: Good Morning Dannon this may not be a cost effective way of sharing data, cloud amazon charges $0.120 per GB data transfer, is there a work around ? also does that mean a worker node cannot communicate with master instance directly and use same below protocol to share history ? Thanks msapre From: Dannon Baker dannon.ba...@gmail.com Date: Tuesday, November 19, 2013 4:55 PM To: System Administrator msa...@nmdp.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] unable to share dataset history Hi, That sort of sharing only works within a single galaxy instance; users are not shared between different galaxies. To copy an entire history from one instance to another you will want to use the history export/import functionality. History context menu - Export to file on the source instance, and Import from file on the destination. -Dannon On Tue, Nov 19, 2013 at 11:20 AM, Manisha Sapre msa...@nmdp.org wrote: Hello Team Galaxy trying to share/ forward dataset history from user 1 ( running on a local instance,Scrn.1) to user 2 (running on cloud amazon ec2 instance,Scrn.2) and *vice-versa*, error:- user is not a valid galaxy user. getting this error while both the users are logged into system and both the instance's are running normal. insights of team will be very helpful. Thanks msapre ___ 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] unable to share dataset history
On Wed, Nov 20, 2013 at 9:07 AM, Manisha Sapre msa...@nmdp.org wrote: apologies if the second question was not framed properly, but it seems there is a fee to share output datasets between nodes on same master instance ? No. ___ 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] hierarchical ObjectStore - noatime
On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening bjoern.gruen...@gmail.comwrote: The new discs will be type=distributed id=primary and the old disc will become type=disk id=secondary. If I understood correctly the old disc is them in some read-only state and will not touched until the primary discs are full or not working ... Correct -- the default HierarchicalObjectStore always writes new files to the first ObjectStore but can read through to any of them. Probably worth noting that, with this base implementation (that could easily be extended to do whatever you'd prefer), when the first objectstore gets full it still won't attempt to write to the second. Is it save to mount the old discs or all discs with noatime, to get a small performance gain? Is Galaxy using noatime? I do believe we're using it, but Nate would be better able to comment on the actual performance gain we see. ___ 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] tiff files in galaxy
If you wanted to implement fancier tiling and display for tiff, the extension point for this would be in the datatype's display_data method. You can use this to do whatever you'd like, displaying an intermediate page with relevant code for tiling, etc. See datatypes/tabular.py's display_data method for an example of the chunking tabular display. On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: I was planning to use server code to tile the large images and then use one of a number of JavaScript libraries to render. Any browser should work without extensions . Jim did this with visigene in the genome browser years ago. - Robert On Dec 3, 2013, at 9:16 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hi, Robert As far as I know, all browsers besides Safari aren't set up to render tiff files by default. Are you using Safari to display the files in Galaxy? There are extensions for Firefox and Chrome that will allow you to display these files. Would that be an option? As a side note: creating, saving, and manipulating images and thumbnails would require Galaxy including a server side image processing library as a dependency. I'd like to do this at some point in the future as it would allow us other advantages too. Thanks, Carl On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access. ___ 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/ ___ 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] How to get an API key during execution?
Hi Neil,
You'll want to look at the users API controller, specifically the api_key
method. Your downstream tool could, upon receiving an empty API key from
the wrapper, generate a new key and use it (after which it'd also be
available to the user).
On Thu, Dec 5, 2013 at 9:05 PM, neil.burd...@csiro.au wrote:
Hi,
I know that if I put :
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
in my tools xml file I am able to get the current api key.
The xml calls my python script with this value, which i then use to
execute workflows via the API.
However, if this is value empty/blank is there a way I can generate an api
key it from within my python script. i.e. is there a method I can call
which would generate this for me?
Thanks
Neil
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Re: [galaxy-dev] cloudlaunch - Can't ssh or ping
If this is an older account then it shouldn't be the VPC issue. I just attempted to ssh to it and it does respond fine for me -- what are the permissions for the cloudman_keypair.pem? `chmod 700 ~/Downloads/cloudman_keypair.pem` and try again. If that doesn't work, you may want to try using something like `ssh -vvv ~/Downloads/cloudman_keypair.pem ubuntu@instance` to get more verbose logging. On Mon, Dec 16, 2013 at 10:48 AM, greg margeem...@gmail.com wrote: I last used cloud launch a year ago with this account. I may have used biocloudcentral though at that point. Is there a work around I can do in the meantime, or should I wait for your fix? On Mon, Dec 16, 2013 at 10:34 AM, Dannon Baker dannon.ba...@gmail.com wrote: Have you previously used cloudlaunch with success with this account? If not, is this a new account created after 12-04-2013? AWS now defaults new accounts to using EC2-VPC (and it doesn't look like there's any way to switch back to EC2 classic) and this unfortunately conflicts with cloudman's security groups -- a known issue that I'm working on a fix for. -Dannon On Mon, Dec 16, 2013 at 10:20 AM, greg margeem...@gmail.com wrote: Hi guys, I just did a cloud launch of MSG by going here: https://usegalaxy.org/cloudlaunch I downloaded the pem file as instructed and I can access the galaxy admin page now. However when I try to ssh into it: $ ssh -i Downloads/cloudman_keypair.pem ubu...@ec2-54-196-189-227.compute-1.amazonaws.com ssh: connect to host ec2-54-196-189-227.compute-1.amazonaws.com port 22: Operation timed out And the same problem when I use the IP address. I also can't ping the above address nor the IP address. It just says request time out. Thanks, Greg ___ 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] Bug: Toolbox filters not applied in workflows
This sounds like a bug; the primary toolbox and workflow editor toolbox should reflect the same set of tools (exception being workflow-specific control steps, etc). I've created a trello card to track this issue here: https://trello.com/c/3TxFHkYR That said, do note the warning on the dynamic toolbox filters page: [image: !] Filters will only hide Tools from the User Interface, they are still available and can be made visible by means of HTML manipulation. That said these feature is not a security feature, it is intended to separate multiple groups of Tools and simplify the ToolBoxhttps://wiki.galaxyproject.org/ToolBox . On Tue, Dec 17, 2013 at 6:27 PM, Eric Rasche rasche.e...@yandex.ru wrote: I'm running the stable copy of galaxy and noticed that some custom, administrative tools (and otherwise tools which should be restricted in access due to licensing/etc.) were showing up in normal user's toolboxes inside the workflow editor. I feel that this is a bug, as the tool filters should be applied globally and not just in terms of what tools users are restricted from seeing in the normal toolbox. For me, this presents a problem as I strongly believe any administrative tools that exist should leak as little information as possible--not their entire set of options and associated documentation. Additionally, that sort of information leakage isn't acceptable by my organisation's policies. Do I have my instance misconfigured or is this an actual bug? I have my galaxy configured according to https://wiki.galaxyproject.org/Admin/Config/Access%20Control $ hg head changeset: 11242:9d4cbf2a1c13 branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu n...@bx.psu.edu date:Fri Dec 06 16:28:31 2013 -0500 summary: Add missing destination long arg to cli runner's Torque plugin and fix an incorrectly used PBS option in the sample job conf. changeset: 11216:c458a0fe1ba8 parent: 11213:6d633418ecfa parent: 11215:f79149dd3d35 user:Nate Coraor n...@bx.psu.edu n...@bx.psu.edu date:Mon Nov 04 14:56:57 2013 -0500 summary: Merge security fix for filtering tools from stable/next-stable. $ hg summary parent: 11242:9d4cbf2a1c13 tip Add missing destination long arg to cli runner's Torque plugin and fix an incorrectly used PBS option in the sample job conf. branch: stable commit: 4 modified, 34 unknown update: (current) Thank you, Eric Rasche Programmer II Center for Phage Technology Texas AM University ___ 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] Cloud Launch - Where is /mnt/galaxyData
With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected. -Dannon On Fri, Dec 20, 2013 at 1:53 PM, greg margeem...@gmail.com wrote: Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunch and chose data cluster when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg ___ 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] Cloud Launch - Where is /mnt/galaxyData
Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly. If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff. On Fri, Dec 20, 2013 at 2:13 PM, greg margeem...@gmail.com wrote: Thanks. I was wrong before. I actually do see a /mnt/galaxyData. Should I not being seeing that? Am I not on cloudman 2.0? -Greg On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker dannon.ba...@gmail.com wrote: With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected. -Dannon On Fri, Dec 20, 2013 at 1:53 PM, greg margeem...@gmail.com wrote: Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunch and chose data cluster when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg ___ 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] Cloud Launch - Where is /mnt/galaxyData
And is this a new instance you've just launched? If so, how'd you launch it? On Fri, Dec 20, 2013 at 2:37 PM, greg margeem...@gmail.com wrote: Here's what I'm seeing: ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker dannon.ba...@gmail.com wrote: Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly. If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff. On Fri, Dec 20, 2013 at 2:13 PM, greg margeem...@gmail.com wrote: Thanks. I was wrong before. I actually do see a /mnt/galaxyData. Should I not being seeing that? Am I not on cloudman 2.0? -Greg On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker dannon.ba...@gmail.com wrote: With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected. -Dannon On Fri, Dec 20, 2013 at 1:53 PM, greg margeem...@gmail.com wrote: Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunchand chose data cluster when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg ___ 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] Cloud Launch - Where is /mnt/galaxyData
Hey Greg, Sorry about the delay on this over the holidays. I see what you're working with now. If you install your customizations in a portable manner in /mnt/galaxyData that should be safe and we'll make sure to provide a smooth migration path going forward should that change. Only 'galaxy' type clusters will have /mnt/galaxy and data only clusters should continue to work just fine with /mnt/galaxyData. -Dannon On Mon, Dec 30, 2013 at 1:33 PM, greg margeem...@gmail.com wrote: Just following up on this. So it's ok to do all of my customizations in /mnt/galaxyData? Or am I doing something wrong, and I need to figure out how to boot up into a version that has /mnt/galaxy? Thanks again, Greg On Fri, Dec 20, 2013 at 2:49 PM, greg margeem...@gmail.com wrote: Yes, I just launched it a few hours ago. I just went here and filled out the form: https://usegalaxy.org/cloudlaunch I chose data cluster when prompted and enter 5GB. On Fri, Dec 20, 2013 at 2:48 PM, Dannon Baker dannon.ba...@gmail.com wrote: And is this a new instance you've just launched? If so, how'd you launch it? On Fri, Dec 20, 2013 at 2:37 PM, greg margeem...@gmail.com wrote: Here's what I'm seeing: ubuntu@ip-10-182-195-79:/$ ls / bin boot dev etc export home initrd.img lib lib64 lost+found media mnt opt proc root run sbin selinux srv sys tmp usr var vmlinuz ubuntu@ip-10-182-195-79:/$ ls mnt cm galaxyData lost+found transient_nfs ubuntu@ip-10-182-195-79:/$ ls /mnt/galaxyData/ export files tmp upload_store On Fri, Dec 20, 2013 at 2:20 PM, Dannon Baker dannon.ba...@gmail.com wrote: Does /mnt/galaxy exist, and does it have all of the expected galaxy components? /mnt/galaxyData might exist, but it should be either empty or a symlink to /mnt/galaxy if I remember correctly. If you're launching your cluster from usegalaxy.org/cloudlaunch, you should always be using the latest stuff. On Fri, Dec 20, 2013 at 2:13 PM, greg margeem...@gmail.com wrote: Thanks. I was wrong before. I actually do see a /mnt/galaxyData. Should I not being seeing that? Am I not on cloudman 2.0? -Greg On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker dannon.ba...@gmail.com wrote: With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have been merged to a single 'galaxy' volume. /mnt/galaxy is now your single persistent (by default, at least) volume, so, if you install your tool to here and share everything should work as expected. -Dannon On Fri, Dec 20, 2013 at 1:53 PM, greg margeem...@gmail.com wrote: Hi guys, I just launched an instance from https://usegalaxy.org/cloudlaunch and chose data cluster when prompted. Everything seems to have gone ok, but when I ssh in, I don't see /mnt/galaxyData Background: Basically we have a bioinformatics tool that needs SGE to run. So I want to install it on a galaxy cloud instance and then provide the share string to other researchers. I did this successfully a year or two ago by installing it to /mnt/galaxyData. Thanks, Greg ___ 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] I can't use API to create a user!
The changes you're looking at are in galaxy-central, and I'm assuming your
local codebase is tracking galaxy-dist, our release repository. You can
wait for these changes to propagate through our release process over to
galaxy-dist (I think this is scheduled to happen in early February), or, if
this is functionality you need right now and you're willing to risk a
little bit of instability using the development repository you can always
pull changesets from galaxy-central.
-Dannon
On Thu, Jan 9, 2014 at 11:04 PM, xlwang xlwang_0...@163.com wrote:
When I use API to create a user, I get an error!
The command is:
#curl -d '{username:test,password:test,email:1...@123.com}'
http://myip:8080/api/users?key=my_key
I get some information:
And I find the api controller source code of users in my galaxy instance,
it's different with the source in api document.
This is mine:
And this is the document:
I don't understand how it happens.Please tell me how to fix it.Thank you!
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截图3.png截图2.png截图1.png___
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Re: [galaxy-dev] Linking Data Files
On Wed, Jan 15, 2014 at 3:04 PM, Cantarel, Brandi L. brandi.canta...@baylorhealth.edu wrote: I can see where I can upload libraries from the galaxy server, but I can’t figure out how to load the “available” data (fastqs) — to clarify instead of asking users to upload 5GB fastq files, which are already on the galaxy server, I would like for users to be able to “see” that data when setting up their pipeline without having to upload the data (ie use Get Data). Is this possible? When I search, I can only see how to do this for “Data Libraries”. Data Libraries are probably the right way to handle this. If you have a large set of fastq data, would it be sufficient to load it all into a data library accessible to your users? Then the user would just have to browse the data library, click import to current history, and they're off and running. -Dannon ___ 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] after update unable to login
Hey Sheldon, My first guess is that something's going wrong with your nginx proxy/cookie configuration. Did you happen to change this when you updated the galaxy server at all? Have you checked the steps at https://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy and verified that (if you're serving from a subdirectory) you have cookie_prefix set? -Dannon On Tue, Jan 14, 2014 at 1:20 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca wrote: Hi, I’ve tried reinstalling from scratch in case there was a problem when I updated the last time. I am still having trouble logging in. The “broken pipe” error message has nothing to do with the failed logins. The logins are successful as far as authentication goes ( I get no error message, if I put in the wrong password I do get an error message ). However, after login the user is redirected to the last page they were on and does not appear to be logged in (no history, clicking on user gives the login or register options). If I sent logins so that anonymous logins are not allowed I always get sent back to the login page. I’ve looked through the archives for a similar problem and not found anything relevant. I’ve tried using the stable version of the latest build as well as the development version. No joy on either. Is there something I’ve missed? Thanks, -Sheldon *From:* Briand, Sheldon *Sent:* Thursday, January 09, 2014 2:26 PM *To:* 'galaxy-dev@lists.bx.psu.edu' *Subject:* after update unable to login Hi, I had a working local install of galaxy. I wanted to install gatk2 and wasn’t able to install it. I upgraded and I am now unable to log in to galaxy. I should note that I am relatively new to galaxy. I had a previously logged in admin session (before the update). So I am able to see that galaxy (after the update) believes, by checking the manage users admin page, I have newly logged in on another browser. The session, however, shows no indication that I am logged in other than not showing an error. Usually I end up back at the last page I was viewing before I logged in. Clicking on user doesn’t show me as logged in, I have no history, and there is no admin tab. I have a nginx proxy setup. Paster.log shows a “Broken pipe” error when I login from nginx. I show no error when I log in directly via the galaxy server. The results are the same. I upgraded from database version 115 to version 117. Is there an easy fix? Thanks, -Sheldon *Sheldon Briand* NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.bri...@ssc-spc.gc.ca ___ 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] allow_user_impersonation (was: creating a hierarchy of students teachers and courses)
Imagine that, actually two cards for it! On Thu, Jan 16, 2014 at 8:33 AM, John Chilton chil...@msi.umn.edu wrote: Card exists and it has 10 votes, that is the most I have seen in a while. https://trello.com/c/zwqNwflD I have added myself as a member to the card, I will see if I can find some time to work on this. -John On Thu, Jan 16, 2014 at 7:27 AM, Dannon Baker dannon.ba...@gmail.com wrote: On Thu, Jan 16, 2014 at 3:39 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: allow_user_impersonation does not work when using external authentication. Are there any fixes for this in progress? If not shall I create a Trello card? If there's no Trello card for it, I doubt it's currently being worked on. And, of course, feel free! -Dannon ___ 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] Can't view file_name in histories via API unless admin?
Hi Niel, Galaxy does not expose filepaths to non-admin users intentionally. For executing a workflow with that particular script, the 'file_id' in question in that example should be an hda, which is what api/history/contents will display for your users as the 'id' for each history item. -Dannon On Fri, Jan 17, 2014 at 6:12 AM, neil.burd...@csiro.au wrote: Hi Charles, not a problem. In my previous post I specified the command line: /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 The api_key in your question refers to the api_key of an admin user, however, the history_id (ebfb8f50c6abde6d) refers to a history not owned by the admin user using the unique api_key i.e. another user, hence the error message I hope that answers your question? Neil From: Charles Girardot [charles.girar...@embl.de] Sent: Friday, January 17, 2014 6:31 PM To: Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Neil, sorry, this is not an answer to your post, I hope you won t mind me stepping in your thread this way. Your message kept my attention because of your note: I am surprised by the error message you report when trying to use an admin API key. How does galaxy know the user who is making the call? Sorry if I am missing the obvious bw Charles On 17 Jan 2014, at 07:35, neil.burd...@csiro.au wrote: Hi, it seems that the entry file_name: does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin user in the universe_wsgi.ini i.e. admin_users = t...@test.com,te...@test.com is this known? Is there anyway to get around this as we don't want all users to be admin, however, they need access to this field. Note that you can't use an admin's api_key as you'll get the error Error in history API at listing dataset: History is not owned by the current user Thanks Neil ___ 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/ ___ 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] Can't view file_name in histories via API unless admin?
Hey Neil, While poking through a few options for you, I remembered we added 'expose_dataset_path' to universe_wsgi.ini. If you're comfortable with users knowing full pathnames, you can enable this 'expose_dataset_path = True' and everyone will be able to see their full paths. -Dannon On Sat, Jan 18, 2014 at 9:37 PM, neil.burd...@csiro.au wrote: Thanks Dannon, Apologies for the length of the email, I'll try and be as succint as possible. I am using Galaxy as a tool for medical image processing. We have a number of organisations (researchers and clinicians ) who would like to use the medical imaging tools we have developed, so are using Galaxy to make them available to the whole community. The researchers and clinicians would just prefer to select a file press execute and then everything would be done i.e. uploaded, processed, results returned. I've managed to achieve this (using a test account which is an admin user). In summary, using John Chilton's multi-file branch of Galaxy, the user can select multiple files and then presses execute. The code(and workflows) then upload all the files selected, splits them into smaller datasets (as the tool only needs 2 input files - for example the user may upload 0179_AV45.hdr, 0179_AV45.img, 0279_AV45.hdr, 0179_AV45.img, 0199_AV45.hdr and 0199_AV45.img, given these 6 input files; 3 datasets will be created based on the filenames i.e. 0199_AV45.hdr and 0199_AV45.img will be in one dataset etc). Another tool is responsible for batching and executing the medical imaging tool with each of these 3 datasets, and finally all the results are returned and then emailed back to the user ( so no user interaction is required other than selecting files and pressing execute) This all worked fine as an admin user, but as a non admin user we are unable to get the file_name from the /api/histories/contents/ etc... being upload for the dataset_id.dat. We need to get the history id of that datase_id.dat filename so we can execute the workflow. As admin, I have a script that is able to get get all the files uploaded (under/histories/contents/etc ...) and then examine each history id to get the file_name and match it with the name that we just uploaded. From this we could then get the history_id. But seen as we can't get hold of the file_name unless your an admin user. Do you know how we can get hold of the history_id of the filename i.e. we can't just assume it's the last entry in /history/contents. So given only a database_'id'.dat filename how can I get the history id dynamically with no user interaction and not being an admin user? Thanks for any help Neil p.s. do you know where in the code it stops file_name from being displayed (using the scripts/api/display.py script) -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Saturday, January 18, 2014 12:34 AM *To:* Burdett, Neil (CCI, Herston - RBWH) *Cc:* charles.girar...@embl.de; Galaxy Dev *Subject:* Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Niel, Galaxy does not expose filepaths to non-admin users intentionally. For executing a workflow with that particular script, the 'file_id' in question in that example should be an hda, which is what api/history/contents will display for your users as the 'id' for each history item. -Dannon On Fri, Jan 17, 2014 at 6:12 AM, neil.burd...@csiro.au wrote: Hi Charles, not a problem. In my previous post I specified the command line: /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 The api_key in your question refers to the api_key of an admin user, however, the history_id (ebfb8f50c6abde6d) refers to a history not owned by the admin user using the unique api_key i.e. another user, hence the error message I hope that answers your question? Neil From: Charles Girardot [charles.girar...@embl.de] Sent: Friday, January 17, 2014 6:31 PM To: Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Neil, sorry, this is not an answer to your post, I hope you won t mind me stepping in your thread this way. Your message kept my attention because of your note: I am surprised by the error message you report when trying to use an admin API key. How does galaxy know the user who is making the call? Sorry if I am missing the obvious bw Charles On 17 Jan 2014, at 07:35, neil.burd...@csiro.au wrote: Hi, it seems that the entry file_name: does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin
Re: [galaxy-dev] html output with javascript
Hi Laure,
This is intentional behavior; galaxy sanitizes all html output as a
security measure by default. You can turn this off on your instance by
changing sanitize_all_html to False in your universe_wsgi.ini.
There's a Trello card to track implementation of allowing administrators to
individually pick which tools to trust, which you can see (and vote for, or
follow) here: https://trello.com/c/8iMhKlPX
-Dannon
On Wed, Feb 5, 2014 at 9:44 AM, Laure QUINTRIC laure.quint...@ifremer.frwrote:
Hello galaxy users,
one of my tools returns an html output in which I have links to images and
javascripts.
Images and Javascripts of the dataset_XXX.dat file are located in a
dataset_XXX_files directory. Images are well displayed in galaxy output but
javascripts aren't executed. Even an alert('foo') cannot be retrieved.
Has somebody already experiment this ? In other related posts, it's said
to look at rgenetics fastqc wrapper but no javascript fonctions are called
in the fastqc_report.html.
Thanks,
Laure
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Re: [galaxy-dev] mpileup - ImportError: cannot import name stylesheet_link_tag
Galaxy was recently updated to use a newer version of webhelpers, version 1.3, in which the signatures of those methods have changed. It looks like you're running a newer version of webhelpers (thus stylesheet_link_tag not being found), but an older version of galaxy. I'm not sure how this would be the case, but is it possible for you to update your galaxy and run with a clean environment (using galaxy's provided webhelper egg), to see if this resolves your issue? -Dannon On Fri, Feb 7, 2014 at 12:11 PM, Adhemar azn...@gmail.com wrote: Hi! I was running mpileup and it's showing the error bellow. The strange thing is that 'galaxy/web/framework/helpers/__init__.py' is trying to import 'stylesheet_link_tag' and it's not available in the webhelpers I've installed for both python versions 2.6.6 or 2.7.3 Could you help me with this? Thanx, Adhemar Traceback (most recent call last): File ./scripts/set_metadata.py, line 29, in module import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/model/__init__.py, line 23, in module import galaxy.datatypes.registry File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/registry.py, line 5, in module import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, graph File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/data.py, line 2, in module import metadata File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/metadata.py, line 24, in module from galaxy.web import form_builder File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/__init__.py, line 4, in module from framework import expose File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/__init__.py, line 28, in module import helpers File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/helpers/__init__.py, line 4, in module from webhelpers import date, stylesheet_link_tag, javascript_include_tag, url_for ImportError: cannot import name stylesheet_link_tag ___ 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] (OperationalError) no such column: history_dataset_association.extended_metadata_id
On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote: This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Yes, I've seen this before when I've killed (or otherwise crashed) a migration in process; migrate_tmp doesn't get automatically cleaned up -- and, to allow for recovery, probably shouldn't.Any idea what may have caused it in your case?For a development database I've most commonly just deleted the migrate_tmp table manually and rerun the migration. It's worth noting that *only* sqlite can have this problem, due to the way migrations work. -Dannon ___ 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] Running out of memory on data download
My first guess is that it's likely this is due to 'debug = True' being set in your universe_wsgi.ini. If you set this to false and restart, the entire request will no longer be loaded into memory. -Dannon ___ 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] ImportError: No module named json
The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ 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] ImportError: No module named json
Got it. We dropped the simplejson egg during the last release (and any you find are holdovers from previous versions of galaxy) in favor of the stdlib module. The relevant module from your find would have been simplejson-2.1.1, and the rest are unrelated. If possible, I'd *really* recommend updating the python version on those nodes as future galaxy developments and tools may count on python 2.6+ (and not just for json, but syntax changes) being available. Other than that, for those affected tools, you may want to manually revert the changes in revision 11967:0c5e20558f6b and add simplejson back into your galaxy. That said, I'm working on adding the anyjson dependency that will allow json to fail through to any installed json library (whether stdlib, simplejson, etc), and that'll be available in galaxy-central reasonably soon. On Thu, Feb 20, 2014 at 2:51 PM, Fenglou Mao feng...@gmail.com wrote: It is a little complicated here, The Galaxy server itself is running CentOS 6 with python 2.6, but the cluster nodes are running CentOS 5 with python 2.4. Mose jobs are running in the cluster nodes. My questions is: if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it up? If we can do this, then we don't need to upgrade the cluster nodes, which is very difficult here. Fenglou On 20 February 2014 13:47, Dannon Baker dannon.ba...@gmail.com wrote: The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ 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] Empty history pane
If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski liisa.ko...@basf.com wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ 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] Empty history pane
Good to hear you've worked around it! For future reference, in Firefox you can open the javascript console by clicking the Firefox (menu at the top)-Web Developer-Web Console. That, or Control/Command+Shift+K. On Fri, Mar 14, 2014 at 1:49 PM, Liisa Koski liisa.ko...@basf.com wrote: Our use was using the lastest Firefox release. I asked him to try FireFox Portable and that seemed to do the trick. It was a problem with his Firefox install. Thanks for you help, Liisa From:Dannon Baker dannon.ba...@gmail.com To:Liisa Koski liisa.ko...@basf.com Cc:Galaxy Dev galaxy-dev@lists.bx.psu.edu Date:13/03/2014 06:39 PM Subject:Re: [galaxy-dev] Empty history pane -- If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski *liisa.ko...@basf.com*liisa.ko...@basf.com wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ 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/* http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: *http://galaxyproject.org/search/mailinglists/*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] I can't impersonate an user
Hi Ricardo, My guess is that you're running into an issue that was fixed in 694411e94d9a. Can you verify the URL that's being pinged by the impersonate dropdown is (in)valid? If so, pulling from stable should fix your issues. -Dannon On Mon, Mar 17, 2014 at 11:24 AM, Perez, Ricardo ricky_...@neo.tamu.eduwrote: Dear all, We are currently using the stable build of Galaxy and we are encountering the following problem: When we try to impersonate an user, the user drop down menu hangs in looking up the user. In consequence, we can not impersonate the user. This behaviour started when we upgraded to the Feb 10, 2014 version. Do we have to modify a configuration file to make this to work again? Thank you all, --Ricardo Perez ___ 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] I can't impersonate an user
It isn't in galaxy-dist (yet), but it is in the stable branch of
galaxy-central, which is safe to pull into a galaxy-dist based repository.
-Dannon
On Tue, Mar 25, 2014 at 10:13 AM, Eric Kuyt erick...@gmail.com wrote:
Hi Dannon,
could this still be existent in galaxy-dist?
Impersonate.makohttps://bitbucket.org/galaxy/galaxy-dist/src/29ce93a13ac7c4a5d2b54e5e2c10960f30a350b3/templates/admin/impersonate.mako?at=default
doesn't seem to have ${h.url_for(controller=/api/users,
action=index)} in its source and tries to find /api/user on the server
root.
Thanks,
Eric
On 17 March 2014 16:31, Dannon Baker dannon.ba...@gmail.com wrote:
694411e94d9a
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Re: [galaxy-dev] restarting multiple web workers
On Tue, Apr 1, 2014 at 2:48 PM, Langhorst, Brad langho...@neb.com wrote: However, when i add a new tool - it does not alway show up (only for one of the workers maybe?) I don't have good answers for the rest of your questions (I'm sure someone else can chime in), but I do have some information about this. You're correct in that, currently, the only process that will reflect the new or reloaded tool is the one the admin user was actually interacting with. While it doesn't solve your problem right now, I've been working on new mechanisms for reloading tools and generally interacting with multiple processes that will be available soon. -Dannon ___ 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] ENA SRA data retrieval with Cloudman
Hey Mo, Sorry for the super delayed response here. I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume. It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section: tool file=data_source/ebi_sra.xml / -Dannon On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the Get Data menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian ___ 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] ENA SRA data retrieval with Cloudman
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes. Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? With everything headed to the toolshed, hopefully this is a thing of the past very soon. The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial In short, you'll need to: 1) ssh to your cloud galaxy instance 2) navigate to /mnt/galaxy/galaxy-app 3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3): tool file=data_source/ebi_sra.xml / 4) Close down ssh, 5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service. One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea. I'll try to document this better. Thanks again, Dannon! Anytime, thanks for your patience and for using Galaxy/Cloudman! ___ 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] krona to metaphlan patch
Hey Brad, thanks for this! I've added these to the metaphlan toolshed repository as-is, and will be adding tests shortly. On Tue, Apr 8, 2014 at 1:24 AM, Langhorst, Brad langho...@neb.com wrote: I'm running with these local additions to Dannon's metaphlan repo. I think it would be better to add these to the current metaphlan repo than to release them standalone. ___ 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] how to delete datasets or save space on local galaxy
Hey, sure. The option you're looking for is allow_user_dataset_purge, around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. Thank you so much! Best, Xiaofei ___ 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/ inline: Screen Shot 2014-04-11 at 4.30.18 PM.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/
