[galaxy-dev] Timeout for job submission
Hello, In my configuration, I submit job through SGE. I have a cluster in the backend. If nodes are shutdown job is in state queue wait and I noticed that it disappear sometime. Is there a timeout somewhere in galaxy which is monitoring jobs ? In fact, I whish to use a script in SGE which is halting or booting nodes according to the SGE queue. -Regards Rem. ___ 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] only showing first lines of large output file
Hello, I am observing some difficulties running a custom tool (processing an sff file). It shows up in Galaxy, runs and its three output files are given back. Only one of them is only showing the first 12 lines of many more... More symptoms: * The corrupted file is written successfully to disk as temp file in the galaxy tmp directory * Something goes wrong while transfering the file to the galaxy data dir (files/001), because while the tool is running the dataset_XX file is shown (as empty file), but after the other outputs are moved this file is gone * in galaxy only a snippet is shown, while the actual datafile is not on disk I would be happy to receive feedback on how to start debugging and solving this issue. Thanks! Mattias -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy in a frame?
On Nov 11, 2011, at 8:32 PM, Oren Livne wrote: Dear All, We are trying to integrate Galaxy with our web app, and we thought of having our web app as the main front end, and allow users to open an HTML frame with Galaxy in it within that app. However, Galaxy makes it impossible - it takes over the entire page when a user logs in or clicks on most links. Is it possible to embed Galaxy in another webapp or is it only designed as a standalone app? Hi Oren, Galaxy is designed to run as a standalone app. There are various ways for other applications to interact with Galaxy which may be suitable for your purposes. --nate Thanks so much, Oren ___ 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] Timeout for job submission
On Nov 14, 2011, at 3:54 AM, remy d1 wrote: Hello, In my configuration, I submit job through SGE. I have a cluster in the backend. If nodes are shutdown job is in state queue wait and I noticed that it disappear sometime. Is there a timeout somewhere in galaxy which is monitoring jobs ? In fact, I whish to use a script in SGE which is halting or booting nodes according to the SGE queue. Hi Rem, Galaxy interfaces with the queue much like qstat does. There should be no timeout, it will simply continue to poll for the state of jobs until they are in a terminal state (or are no longer listed in the list of jobs currently known by SGE). --nate -Regards Rem. ___ 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] jquery script error
I have have discovered that this error is not unique to the number of files I
am linking. It has been reported from several of my users that there is a
similar issue with Internet Explorer 8.
Step 1: Import shared data into history: One user tried to import data from a
shared library into her history. Internet Explorer puts up an ugly message
“Stop running this script?” Complaining that continuing to run the script will
cause her machine to stop functioning. Sometimes the display seemed to get
truncated, only displaying a subset of the available datasets. The import
seemed to work OK, though.
Step 2: Debug the issue using IE built-in script debugger. I was able to
replicate the issue and ran some minor debugging from within IE. The results
of this are as follows:
Error Message: Windows Internet Explorer
Stop running this script?
A script on this page is causing Internet Explorer to run slowly.
If it continues to run, your computer might become unresponsive.
Debugging results: Line: 1
Error: jQuery, MooTools or Prototype needs to be loaded before jStorage!
(function(f){if(!f||!(f.toJSON||Object.toJSON||window.JSON)){throw new
Error(jQuery, MooTools or Prototype needs to be loaded before jStorage!)}var
g={},d={jStorage:{}},h=null,j=0,l=f.toJSON||Object.toJSON||(window.JSON(JSON.encode||JSON.stringify)),e=f.evalJSON||(window.JSON(JSON.decode||JSON.parse))||function(m){return
String(m).evalJSON()},i=false;_XMLService={isXML:function(n){var
m=(n?n.ownerDocument||n:0).documentElement;return
m?m.nodeName!==HTML:false},encode:function(n){if(!this.isXML(n)){return
false}try{return new XMLSerializer().serializeToString(n)}catch(m){try{return
n.xml}catch(o){}}return false},decode:function(n){var m=(DOMParser in
window(new
DOMParser()).parseFromString)||(window.ActiveXObjectfunction(p){var q=new
ActiveXObject(Microsoft.XMLDOM);q.async=false;q.loadXML(p);return
q}),o;if(!m){return false}o=m.call(DOMParser in window(new
DOMParser())||window,n,text/xml);return this.isXML(o)?o:false}};function
k(){if(localStorage in
window){try{if(window.localStorage){d=window.localStorage;i=localStorage}}catch(p){}}else{if(globalStorage
in
window){try{if(window.globalStorage){d=window.globalStorage[window.location.hostname];i=globalStorage}}catch(o){}}else{h=document.createElement(link);if(h.addBehavior){h.style.behavior=url(#default#userData);document.getElementsByTagName(head)[0].appendChild(h);h.load(jStorage);var
n={};try{n=h.getAttribute(jStorage)}catch(m){}d.jStorage=n;i=userDataBehavior}else{h=null;return}}}b()}function
b(){if(d.jStorage){try{g=e(String(d.jStorage))}catch(m){d.jStorage={}}}else{d.jStorage={}}j=d.jStorage?String(d.jStorage).length:0}function
c(){try{d.jStorage=l(g);if(h){h.setAttribute(jStorage,d.jStorage);h.save(jStorage)}j=d.jStorage?String(d.jStorage).length:0}catch(m){}}function
a(m){if(!m||(typeof m!=stringtypeof m!=number)){throw new TypeError(Key
name must be string or numeric)}return
true}f.jStorage={version:0.1.5.0,set:function(m,n){a(m);if(_XMLService.isXML(n)){n={_is_xml:true,xml:_XMLService.encode(n)}}g[m]=n;c();return
n},get:function(m,n){a(m);if(m in g){if(typeof
g[m]==objectg[m]._is_xmlg[m]._is_xml){return
_XMLService.decode(g[m].xml)}else{return g[m]}}return
typeof(n)==undefined?null:n},deleteKey:function(m){a(m);if(m in g){delete
g[m];c();return true}return
false},flush:function(){g={};c();try{window.localStorage.clear()}catch(m){}return
true},storageObj:function(){function m(){}m.prototype=g;return new
m()},index:function(){var m=[],n;for(n in
g){if(g.hasOwnProperty(n)){m.push(n)}}return m},storageSize:function(){return
j},currentBackend:function(){return i},storageAvailable:function(){return
!!i},reInit:function(){var
m,o;if(hh.addBehavior){m=document.createElement(link);h.parentNode.replaceChild(m,h);h=m;h.style.behavior=url(#default#userData);document.getElementsByTagName(head)[0].appendChild(h);h.load(jStorage);o={};try{o=h.getAttribute(jStorage)}catch(n){}d.jStorage=o;i=userDataBehavior}b()}};k()})(window.jQuery||window.$);
jQuery, MooTools or Prototype needs to be loaded before jStorage!
I cannot replicate this with other browsers. I have tried it with Google Crome
and Firefox 3.6.20.
Thanks,
Iry Witham
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Re: [galaxy-dev] Actual User Code
I think the problem has to do with self.app.config.outputs_to_working_directory which dos not jive well with linking files from the admin menu instead of uploading them. It still performs the move (i.e) in lib/galaxy/jobs/__init__.py and moves a link to the actual files and writes over it. Any thoughts on how to fix this. Looks like more of a core bug. if self.app.config.outputs_to_working_directory: for dataset_path in self.get_output_fnames(): try: shutil.move( dataset_path.false_path, dataset_path.real_path ) log.debug( finish(): Moved %s to %s % ( dataset_path.false_path, dataset_path.real_path ) ) From: Oren Livne [mailto:li...@uchicago.edu] Sent: Friday, November 11, 2011 1:33 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Actual User Code Check the permissions of the test.bam file. Maybe the galaxy user can't write into a temp directory when it runs the external_chown_script. On 11/11/2011 3:30 PM, Chorny, Ilya wrote: When I try to link file paths into a shared data library from the admin menu it fails. I get the following in the log file: galaxy.jobs DEBUG 2011-11-11 13:24:38,280 (2645) Changing ownership of working directory with: /usr/bin/sudo -E /home/galaxy/production/Sept06/galaxy-central/sc ripts/external_chown_script.py ./database/job_working_directory/2645 galaxy 504 galaxy.jobs ERROR 2011-11-11 13:24:38,771 fail(): Missing output file in working directory: [Errno 13] Permission denied: '/bioinfoSD/ichorny/test.bam' galaxy.datatypes.metadata DEBUG 2011-11-11 13:24:38,919 Cleaning up external metadata files STDOUT has the following : Job 2645's output dataset(s) could not be read Also my file get erased: /bioinfoSD/ichorny/test.bam Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy in a frame?
Thanks so much, John! Our webapp host is different than the Galaxy host. But I found a way to do it that avoids cross-side scripting via Spring MVC on the server side. So this is possible. Best, Oren On 11/14/2011 12:02 PM, Duddy, John wrote: You can put it in an iframe, and if you are serving it from the same host as your main app, you can also inject javascript/CSS to control certain aspects, such as styling and event propagation related to navigation. However, this is not a trivial exercise. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Oren Livne Sent: Friday, November 11, 2011 5:32 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Galaxy in a frame? Dear All, We are trying to integrate Galaxy with our web app, and we thought of having our web app as the main front end, and allow users to open an HTML frame with Galaxy in it within that app. However, Galaxy makes it impossible - it takes over the entire page when a user logs in or clicks on most links. Is it possible to embed Galaxy in another webapp or is it only designed as a standalone app? Thanks so much, Oren ___ 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] Actual User Code
On Nov 14, 2011, at 2:23 PM, Chorny, Ilya wrote: I think the problem has to do with self.app.config.outputs_to_working_directory which dos not jive well with linking files from the admin menu instead of uploading them. It still performs the move (i.e) in lib/galaxy/jobs/__init__.py and moves a link to the actual files and writes over it. Any thoughts on how to fix this. Looks like more of a core bug. if self.app.config.outputs_to_working_directory: for dataset_path in self.get_output_fnames(): try: shutil.move( dataset_path.false_path, dataset_path.real_path ) log.debug( finish(): Moved %s to %s % ( dataset_path.false_path, dataset_path.real_path ) ) It looks like the central code encounters this bug as well, not sure how it made it this long. I'm working on it now. --nate From: Oren Livne [mailto:li...@uchicago.edu] Sent: Friday, November 11, 2011 1:33 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Actual User Code Check the permissions of the test.bam file. Maybe the galaxy user can't write into a temp directory when it runs the external_chown_script. On 11/11/2011 3:30 PM, Chorny, Ilya wrote: When I try to link file paths into a shared data library from the admin menu it fails. I get the following in the log file: galaxy.jobs DEBUG 2011-11-11 13:24:38,280 (2645) Changing ownership of working directory with: /usr/bin/sudo -E /home/galaxy/production/Sept06/galaxy-central/sc ripts/external_chown_script.py ./database/job_working_directory/2645 galaxy 504 galaxy.jobs ERROR 2011-11-11 13:24:38,771 fail(): Missing output file in working directory: [Errno 13] Permission denied: '/bioinfoSD/ichorny/test.bam' galaxy.datatypes.metadata DEBUG 2011-11-11 13:24:38,919 Cleaning up external metadata files STDOUT has the following : Job 2645's output dataset(s) could not be read Also my file get erased: /bioinfoSD/ichorny/test.bam Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.com Website: www.illumina.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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/
