[galaxy-dev] SLURM timeouts
Hi, I'm running a fork of galaxy-central latest_2014.08.11. The instance is configured to run jobs on a SLURM cluster. The problem is that the SLURM controller sometimes becomes too busy which results in errors like: galaxy.jobs.runners.drmaa INFO 2014-10-23 21:10:47,768 (1813/22896754) job left DRM queue with following message: code 1: slurm_load_jobs error: Socket timed out on send/recv operation,job_id: 22896754 This causes Galaxy to assume that the job has failed: galaxy.jobs.runners ERROR 2014-10-23 21:10:47,881 (1813/22896754) Job output not returned from cluster: [Errno 2] No such file or directory: '/n/regal/stemcellcommons/galaxy-stage/job_working_directory/001/1813/galax y_1813.o' This happens with both galaxy.jobs.runners.drmaa:DRMAAJobRunner and galaxy.jobs.runners.slurm:SlurmJobRunner. Is there any way to handle this condition in Galaxy? Thanks, Ilya ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] $GALAXY_SLOTS is set incorrectly when using LSF
Hi, I've noticed that $GALAXY_SLOTS that was always set to 1 when using LSF. It turns out that LSF specifies the number of parallel slots using $LSB_DJOB_NUMPROC env variable which isn't checked in lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh. A diff that describes the fix is attached. Ilya diff -r 61a3094bd3ed lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Wed May 14 12:15:54 2014 -0400 +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Thu May 15 16:12:04 2014 -0400 @@ -8,6 +8,8 @@ GALAXY_SLOTS=$NSLOTS elif [ -f $PBS_NODEFILE ]; then GALAXY_SLOTS=`wc -l $PBS_NODEFILE` +elif [ -n $LSB_DJOB_NUMPROC ]; then +GALAXY_SLOTS=$LSB_DJOB_NUMPROC else GALAXY_SLOTS=1 unset GALAXY_SLOTS_CONFIGURED ___ 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] Jobs deleted staying in 'dr' status
On 9/12/13 10:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Sep 12, 2013 at 2:01 PM, Mathieu Bahin mathieu.ba...@irisa.fr wrote: Hi all, We have been developing our own Galaxy instance for a while now. We have a cluster on which the job are sent to be executed, it is managed through SGE. Usually, communication between SGE and DRMAA is ok and we don't have any problem with that. When a job is deleted by the user, most of the times, the job disappears but sometimes, we don't know why, the job stays and has the status 'dr' within SGE. If we don't kill it 'manually', it stays forever. It is not always the same tools which produces this error. Have you any idea why how manage it ? I have noticed problem with our DRMMA/SGE setup where a user can cancel a large job (using the job splitter in at least some cases), but Galaxy does not seem to cancel the jobs on the cluster. I've not tried to diagnose this yet - it could be a similar issue though. Also, in our DRMAA/LSF setup (using a fork of the latest galaxy-dist) jobs generated by the current workflow step continue running on the cluster after history is deleted. Ilya ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Dealing with cluster job preemption
Hi, Our Galaxy instance is configured to use LSF. The problem is that sometimes our jobs get preempted (stopped and re-queued to let higher-priority jobs run) and Galaxy thinks that those jobs have failed. Is there any way around that by any chance? Thanks, Ilya ___ 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] Dynamic job runner not being dispatched for a tool
It might be due to this bug:http://dev.list.galaxyproject.org/Limit-number-of-Jobs-to-Trinity-tt4661790.html#a4661874
Ilya
From: Ganote, Carrie L cgan...@iu.edu
Date: Monday, October 7, 2013 1:46 PM
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Dynamic job runner not being dispatched for a tool
Hi List,
I'm a bit baffled by a new tool I've tried to add to Galaxy. The job runner does not dispatch it correctly.
I added the tool via the toolshed, set up the executable on the cluster side, and attempted to hook it up to the dynamic job runner. The destination always ended up set as local.
Works fine if the default runner is pbs, but if it's local by default, it will only dispatch locally.
Attempting to work backwards, I copied the wrapper to a local tool directory, and pared everything down to a minimum to run. There must be something missing. My trinity_all dynamic definition works fine, Newbler doesn't. Is there anything obvious here?
~tool_conf.xml
?xml version=1.0?
toolbox
section name=Assembly id=assembly
tool file=sr_assembly/runAssembly.xml /
tool file=ngs_rna/trinity_all.xml /
/section
!-- I have to have two sections in order for any sections to show up at all --
section name=Send Data id=send
tool file=data_destination/epigraph.xml /
tool file=data_destination/epigraph_test.xml /
tool file=genomespace/genomespace_exporter.xml /
/section
/toolbox
~tools/sr_assembly/runAssembly.xml
tool id=runAssembly name=runAssembly version=1.0.1
descriptionDe novo assembly of Roche/454 reads using Newbler/description
command
runAssembly $sanger_input -o $newbler_metrics
/command
inputs
!-- READSEQ INFILES --
param name=sanger_input type=data format=fasta,fastqsanger label=SE Fasta/Fastq file/
!-- for walltime control --
param name=walltime type=select label=How long will your job need
option selected=true value=18 hrs/option
option value=4848 hrs/option
/param
/inputs
outputs
data name=newbler_metrics format=txt /
/outputs
/tool
~job_conf.xml
?xml version=1.0?
job_conf
plugins workers=4
plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner /
plugin id=pbs type=runner load=galaxy.jobs.runners.pbs:PBSJobRunner /
/plugins
handlers default=handlers
handler id=handler0 tags=handlers/
/handlers
destinations default=local
destination id=local runner=local/
destination id=pbs_normal runner=pbs tags=mycluster
param id=Resource_Listnodes=1:ppn=4,vmem=32gb,walltime=24:00:00/param
/destination
destination id=newbler_d runner=dynamic
param id=typepython/param
param id=functionnewbler/param
/destination
destination id=trinity_d runner=dynamic
param id=typepython/param
param id=functiontrinity_all/param
/destination
/destinations
tools
tool id=runAssembly destination=newbler_d/
tool id=trinity_all destination=trinity_d/
/tools
limits
/limits
/job_conf
~lib/galaxy/jobs/rules/dynamicjobs.py
import os
from galaxy.jobs import JobDestination
def newbler(job):
incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
walltime_para = incoming[walltime]
walltime = int(walltime_para.replace(\,))
params = {}
string = vmem=500gb,nodes=1:ppn=32,walltime=%d:00:00%walltime
params[Resource_List] = string
return JobDestination(runner=pbs, params=params)
def trinity_all(job):
incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
walltime_para = incoming[walltime]
walltime = int(walltime_para.replace(\,))
params = {}
string = vmem=500gb,nodes=1:ppn=32,walltime=%d:00:00%walltime
params[Resource_List] = string
return JobDestination(runner=pbs, params=params)
I re-installed the Roche 454 toolsuite from the toolshed once more to see if it just needed a kick. I copied the tool id into my job_conf file to make sure I made no mistakes on the id. I tried to send it to dynamic job runner and to pbs runner. I pulled and
merged this galaxy about a month ago, so it should be mostly up to date - but I've had so many issues that I may have to just re-install from scratch.
Thanks a ton for any advice,
Carrie Ganote
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[galaxy-dev] Stopping jobs by deleting history via API
Hi, I was wondering if there are any near term plans to fix this issue? https://trello.com/c/Tbota8xG/992-deleting-history-using-the-api-does-not-d elete-stop-jobs Thanks, Ilya ___ 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] Problems with tophat in local instance
Hi, It sounds like the reference genome is not set up for the Tophat tool. Please have a look at the instructions (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) under Tools and Their Corresponding loc Files and Bowtie and Tophat. Ilya From: Rainy Luo xiaolin2...@gmail.com Date: Monday, July 22, 2013 1:33 PM To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Problems with tophat in local instance Hi,all, I am a beginner of Galaxy.Because I need to analyze large-scale NGS data and the pubic Galaxy serve did not work out,I installed linux(the first time to use linux) and set up the local galaxy instance in my computer. It seemed everything worked fine until I tried to use Tophat to align the reads to the reference genome.The problem is although I have already downloaded the Refgenome from UCSC,when I use the Tophat,select a reference genomeoption is empty(please see the attached file). is there anybody having similar problem?How to deal with it? Thanks! Rainy ___ 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 annotations
Awesome, thanks! What about workflows imported from tool shed repositories? For example, I have two annotated workflows in this repository: http://testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test. When I install them from the repository to my local galaxy-central instance (9722:6d72b2db32c0) the annotations are still not showing up in the workflow editor. Ilya On 5/14/13 11:55 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: On the other hand, if a workflow is imported from a file on disk or from a URL, tool level annotations are available while workflow level annotations are not. This has been fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/commits/8882e45504a3/ Thanks for reporting this issue, J. ___ 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 accessing test tool shed repositories
Thanks for getting this fixed so quickly! Ilya On 5/2/13 4:32 PM, Dave Bouvier d...@bx.psu.edu wrote: Ilya, Thank you for reporting this issue, a fix has been committed in 9627:8d8368ab03ff, and the test tool shed has been updated. --Dave B. On 5/2/13 13:01:54.000, Sytchev, Ilya wrote: Hi, I can't install any tools from the test tool shed into the local Galaxy instances. I can see the list of the repositories but nothing happens when I click on any of them. I can still access repositories in the main tool shed. The same thing happens in fresh installations of both galaxy-central and galaxy-dist. Attached screenshot shows a list of Sequence Analysis repositories in the test tool shed (note the lack of buttons). I'd appreciate any help. Thanks, Ilya ___ 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] Teaching using Galaxy
Hi David, These short courses may be of interest: http://scriptogr.am/ohofmann/intro-to-galaxy http://scriptogr.am/ohofmann/rna-seq http://scriptogr.am/ohofmann/exome-seq Ilya On 4/25/13 10:11 AM, David Joly idj...@gmail.com wrote: I was pretty much interested in Bio-Linux. However, the version of Galaxy that comes with it is already outdated and there is no easy way to update it. It is possible to delete it and re-install a newer version, this would be another possibility... Le 2013-04-25 à 05:50, Hans-Rudolf Hotz a écrit : Hi David I have not used or tested it myself yet, but: have you looked into Bio-Linux ? The latest release (Bio-Linux 7) comes with Galaxy pre-installed, see: http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info Regards, Hans-Rudolf On 04/25/2013 12:52 AM, David Joly wrote: Thanks Dave! The focus is clearly more like your second description. The course is not intended to show them how to use command lines, or how to navigate in a UNIX environment and how to program. In fact, I think some would call what I have in mind more of a computational biology course than a bioinformatics course, but I think it is not really important here. I'm thinking of another course to introduce them to the UNIX environment and using Python to script simple programs, but for this one, I'd prefer staying away from a terminal that can be horrifying at first (for most students, black screen = evil) So, the course is about knowing the tools and their basics, and how to use them (in this case using Galaxy as the platform). What is a sequence alignment, why should we do a sequence alignment, how a sequence alignment work, and how can I do one in Galaxy. This is only one example, other (and often inter-related) topics would include BLAST, phylogenetics, sequence polymorphisms, and so on, up to analyzing next-generation sequencing data... Regarding how I'll set my environment, I was thinking of setting a local instance (I have one on my computer right now and I'm already getting familiar with it). The hardware on which I'll set the instance for the course is another issue, but this is not the topic of this email... I'll have a better look at how I could use published histories and workflows... Thanks, DJ 2013/4/24 Dave Clements cleme...@galaxyproject.org mailto:cleme...@galaxyproject.org Hi David, Using Galaxy to teach undergraduates is a long term interest of mine. Which, unfortunately, does not mean I have yet put a lot of thought into it. However, lack of thought hasn't stopped me yet. First, this topic was discussed in a breakout at last year's GCC: http://wiki.galaxyproject.org/Events/GCC2012/Program/Breakouts/Bioinform aticsTraining That's more of a discussion than a set of best practices. What do you want them to spend time learning? Do you want them to learn the (sometimes grinding) details of using the command line, and how to install software and their dependencies on a Linux box? Or do you want to focus mainly on the high level stuff like here is how and why BLAST works, and get some practice using it? I think this question of focus is a central one, and it's one that well-informed people disagree on. Galaxy is a great platform for focussing on the high-level stuff and avoiding the frustration that can come with installing a C compiler, for example. On the other hand, if you really want them to learn the command line, then you might want to start elsewhere. If you do use Galaxy for teaching, there are a couple of ways you could do it. First, I recommend setting up your own server(s) either locally or on the cloud. (The AWS in Education grant program is built just for this case.) If you wanted to teach them a mixture of high-level and low level, you could start them out as users on a shared server, and then later in the course have them setup their own Galaxy on a cloud instance. Also, for Galaxy training we find that published histories, workflows, and Galaxy Pages, are a superb way to create exercises. Hope this helps, Dave C. On Mon, Apr 22, 2013 at 12:30 PM, David Joly idj...@gmail.com mailto:idj...@gmail.com wrote: Hi everybody! I am currently creating a bioinformatics course for undergraduate (biology students with no knowledge of programming). I would like to use Galaxy as their everyday platform where they would learn the basics and use the appropriate tools (BLAST and databases, multiple alignment, phylogenetics, dealing with omics data, and so on). Is there any available resources about using Galaxy for teaching (undergraduates)? Any suggestions of good textbooks? Not a Galaxy textbook of course, but a bioinformatics textbook that would be a good companion
Re: [galaxy-dev] BioBlend: Problem Running Example file
JSONDecodeError will be raised if the given JSON document is not valid. http://simplejson.readthedocs.org/en/latest/ Ilya From: Rob Leclerc robert.lecl...@gmail.com Date: Friday, March 8, 2013 12:01 AM To: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Subject: [galaxy-dev] BioBlend: Problem Running Example file I had trouble running blend4j, so I tried to jump into python (a language I have little experience with). I tried running the example run_import_workflow.py % python run_imported_workflow.py http://localhost:8080 8c25bc83f6f9e4001dd21eb7b64f063f but I get an error: Initiating Galaxy connection Importing workflow Creating data library 'Imported data for API demo' Traceback (most recent call last): File run_imported_workflow.py, line 53, in module library_dict = gi.libraries.create_library(library_name) File build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/libraries/__init__.py, line 27, in create_library File build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/client.py, line 53, in _post File build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/__init__.py, line 132, in make_post_request File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/requests-1.1.0-py2.7.egg/requests/models.py, line 604, in json return json.loads(self.text or self.content) File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/__init__.py, line 454, in loads return _default_decoder.decode(s) File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py, line 374, in decode obj, end = self.raw_decode(s) File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py, line 393, in raw_decode return self.scan_once(s, idx=_w(s, idx).end()) simplejson.scanner.JSONDecodeError: Expecting value: line 1 column 1 (char 0) Is there anything I am missing from the stock configuration which would cause this not to run out of the box? Cheers, Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Downloading datasets without username/password when login is required
Great, thanks John! Ilya On 2/26/13 12:18 AM, John Chilton chil...@msi.umn.edu wrote: I have also encountered the need for this and believe it is important. I have issued a pull request implementing this. https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equ ivalent-of-dataset-display/diff Thanks, -John On Thu, Dec 13, 2012 at 2:20 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote: So, it turns out that it's currently impossible to download datasets programmatically without using username/password (when require_login is set to True) because Galaxy API does not have functionality to download datasets. Are there any plans to implement this feature? Thanks, Ilya On 12/11/12 2:41 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote: Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ 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/ On Thu, Dec 13, 2012 at 2:20 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote: So, it turns out that it's currently impossible to download datasets programmatically without using username/password (when require_login is set to True) because Galaxy API does not have functionality to download datasets. Are there any plans to implement this feature? Thanks, Ilya On 12/11/12 2:41 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote: Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Downloading datasets without username/password when login is required
So, it turns out that it's currently impossible to download datasets programmatically without using username/password (when require_login is set to True) because Galaxy API does not have functionality to download datasets. Are there any plans to implement this feature? Thanks, Ilya On 12/11/12 2:41 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote: Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Downloading datasets without username/password when login is required
Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Uploading Files on Local Cluster Install
LimitRequestBody has a max value of 2147483647 (2GB). You probably want
to set it to zero to disable the limit:
http://httpd.apache.org/docs/current/mod/core.html#limitrequestbody
Also, you may be running into memory limits on the server, especially if
it's running a 32-bit OS (where each process is limited to about 2GB of
memory):
http://stackoverflow.com/questions/1922414/file-upload-limit-in-http
Ilya
On 11/29/12 12:57 PM, greg margeem...@gmail.com wrote:
Hmm, no luck on the large uploads.
I tried using a recent version of Google Chrome.
I added these settings to /etc/httpd/conf/httpd.conf
Timeout 6000
LimitRequestBody 32147483647
And restarted apache.
But when I try to upload a 3.7GB file I get this error in Galaxy:
Bad Gateway
The proxy server received an invalid response from an upstream server.
Now I do see this error in the Galaxy log, so I'm thinking I'm not
hitting an Apache issue, and I'm not hitting a browser issue. Perhaps
it's a paste issue?
Exception happened during processing of request from ('127.0.0.1', 52128)
Traceback (most recent call last):
File
/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.
py,
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/local/python27/lib/python2.7/SocketServer.py, line 323,
in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/local/python27/lib/python2.7/SocketServer.py, line 639,
in __init__
self.handle()
File
/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.
py,
line 432, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/local/python27/lib/python2.7/BaseHTTPServer.py, line
337, in handle
self.handle_one_request()
File
/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.
py,
line 427, in handle_one_request
self.wsgi_execute()
File
/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.
py,
line 287, in wsgi_execute
self.wsgi_start_response)
File
/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py,
line 202, in __call__
return app(environ, start_response)
File
/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/xforwa
rdedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File
/misc/local/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/dep
loy/config.py,
line 164, in __call__
app_iter = self.application(environ, start_response)
File
/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/transl
ogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File
/misc/local/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/eval
exception/middleware.py,
line 226, in __call__
return self.respond(environ, start_response)
File
/misc/local/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/eval
exception/middleware.py,
line 399, in respond
if self.xmlhttp_key in req.params:
File build/bdist.linux-x86_64/egg/webob/__init__.py, line 900, in
params
params = self.str_params
File build/bdist.linux-x86_64/egg/webob/__init__.py, line 892, in
str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File build/bdist.linux-x86_64/egg/webob/__init__.py, line 818, in
str_POST
keep_blank_values=True)
File /usr/local/python27/lib/python2.7/cgi.py, line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File /usr/local/python27/lib/python2.7/cgi.py, line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File /usr/local/python27/lib/python2.7/cgi.py, line 510, in __init__
self.read_single()
File /usr/local/python27/lib/python2.7/cgi.py, line 647, in
read_single
self.read_lines()
File /misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py,
line 268, in read_lines
self.read_lines_to_outerboundary()
File /usr/local/python27/lib/python2.7/cgi.py, line 697, in
read_lines_to_outerboundary
line = self.fp.readline(116)
File
/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.
py,
line 467, in readline
data = self.file.readline(self.length - self._consumed)
File /usr/local/python27/lib/python2.7/socket.py, line 412, in
readline
bline = buf.readline(size)
OverflowError: signed integer is greater than maximum
On Thu, Nov 29, 2012 at 11:26 AM, greg margeem...@gmail.com wrote:
This says Google Chrome can support uploads larger than 4 GB.
http://www.motobit.com/help/scptutl/pa98.htm
Maybe I just need to configure Apache?
I'll let you guys know what I find.
-Greg
On Thu, Nov 29, 2012 at 11:22 AM, greg margeem...@gmail.com wrote:
Follow up question. What's the deal with the 2GB limit it mentions?
I think it would be pretty convienent to allow larger uploads. We're
on a fast local network so even 10 or 20 GB uploads pretty fast.
Can I
Re: [galaxy-dev] galaxy-dev Digest, Vol 77, Issue 31
Here's a link to one of the WIG files I am using: https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip I'd appreciate any pointers. Thanks, Ilya On 11/27/12 3:57 PM, Jim Johnson johns...@umn.edu wrote: Ilya, Could you send me a failing input file, and I'll try to find out what is failing? Thanks, JJ -- Message: 6 Date: Tue, 27 Nov 2012 07:22:30 + From: Sytchev, Ilya isytc...@hsph.harvard.edu To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] No output from IGVtools tile Message-ID: ccd9d465.30c7%isytc...@hsph.harvard.edu Content-Type: text/plain; charset=us-ascii Hi, I'm running IGVtools (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in Galaxy on a WIG file but it's failing with exit code 1 and producing no output file. On the other hand, IGVtools count and sort run successfully in Galaxy on their respective inputs. Also, IGVtools tile tool runs successfully by itself from the command line on the same input WIG file from the same user account that runs this Galaxy instance. Standard out and error from running tile in Galaxy are below. I was wondering if anyone had a similar problem with IGVtools in their Galaxy instance. Thanks, Ilya stdout: Tile. File = input_file.wig Max zoom = 7 Probe file = None Window functions: mean IGV directory: /n/galaxy/home/galaxy_scc/igv INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome loaded Processing chromosome chr19 .10.0% .20.0% .30.0% .40.0% .50.0% ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring data from non-existent locus. Probe = null Locus = chr19:61342442-61342477. chr19 length = 61342430 Group idx: 1 100.0% stderr: cp: cannot stat `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/database/ jo b_working_directory/000/100/output.tdf': No such file or directory ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] No output from IGVtools tile
The error is gone, thank you very much! What was the problem? Ilya On 11/27/12 5:34 PM, Jim Johnson johns...@umn.edu wrote: Ilya, I fixed the igvtools_tile.xml tool config and pushed it to the toolshed. Thanks for finding and reporting the problem. JJ On 11/27/12 3:18 PM, Sytchev, Ilya wrote: Here's a link to one of the WIG files I am using: https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip I'd appreciate any pointers. Thanks, Ilya On 11/27/12 3:57 PM, Jim Johnson johns...@umn.edu wrote: Ilya, Could you send me a failing input file, and I'll try to find out what is failing? Thanks, JJ -- Message: 6 Date: Tue, 27 Nov 2012 07:22:30 + From: Sytchev, Ilya isytc...@hsph.harvard.edu To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] No output from IGVtools tile Message-ID: ccd9d465.30c7%isytc...@hsph.harvard.edu Content-Type: text/plain; charset=us-ascii Hi, I'm running IGVtools (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in Galaxy on a WIG file but it's failing with exit code 1 and producing no output file. On the other hand, IGVtools count and sort run successfully in Galaxy on their respective inputs. Also, IGVtools tile tool runs successfully by itself from the command line on the same input WIG file from the same user account that runs this Galaxy instance. Standard out and error from running tile in Galaxy are below. I was wondering if anyone had a similar problem with IGVtools in their Galaxy instance. Thanks, Ilya stdout: Tile. File = input_file.wig Max zoom = 7 Probe file = None Window functions: mean IGV directory: /n/galaxy/home/galaxy_scc/igv INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome loaded Processing chromosome chr19 .10.0% .20.0% .30.0% .40.0% .50.0% ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring data from non-existent locus. Probe = null Locus = chr19:61342442-61342477. chr19 length = 61342430 Group idx: 1 100.0% stderr: cp: cannot stat `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/databas e/ jo b_working_directory/000/100/output.tdf': No such file or directory ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] No output from IGVtools tile
Hi, I'm running IGVtools (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in Galaxy on a WIG file but it's failing with exit code 1 and producing no output file. On the other hand, IGVtools count and sort run successfully in Galaxy on their respective inputs. Also, IGVtools tile tool runs successfully by itself from the command line on the same input WIG file from the same user account that runs this Galaxy instance. Standard out and error from running tile in Galaxy are below. I was wondering if anyone had a similar problem with IGVtools in their Galaxy instance. Thanks, Ilya stdout: Tile. File = input_file.wig Max zoom = 7 Probe file = None Window functions: mean IGV directory: /n/galaxy/home/galaxy_scc/igv INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome loaded Processing chromosome chr19 .10.0% .20.0% .30.0% .40.0% .50.0% ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring data from non-existent locus. Probe = null Locus = chr19:61342442-61342477. chr19 length = 61342430 Group idx: 1 100.0% stderr: cp: cannot stat `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/database/jo b_working_directory/000/100/output.tdf': No such file or directory ___ 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/
