Re: [galaxy-dev] galaxy and torque - resource allocation
Hello John, This is totally excellent! This gave me a great idea for my little torque installation. I hope you don't mind but I have an unrelated issue with torque that I do not seem to grasp. My issue is that it take a rediculious amount of time to upload a 2Gb file. I tried many different configurations of apache to upload that 2Gb file without success. Galaxy keeps showing that arrow going up constantly (over 12h). And this is an upload from a file located on the server running galaxy. Here is some information from my installation. 1. Server redhat6 with galaxy behind an Apache HTTP Server proxy like described on your website. 2. I have Apache HTTP Server running as the galaxy user with a. Serving Galaxy at a sub directory b. Compression and caching c. Sending files using Apache You will see in attachment my apache's galaxy, deflate, expire and xsendfile configuration file. Furthermore, I've changed the following in galaxy.ini: apache_xsendfile = True upstream_gzip = False Any suggestions? Any information I missed? PLEASE HELP!!! Cordialement / Regards, Edgar Fernandez -Message d'origine- De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : January-21-15 9:34 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Was hoping someone with an actual torque cluster would respond. I think the way you would configure this might be for instance might be setting native_specification like -l nodes=1:ppn=n. Depending on how things are configured or simply because I am ignorant - this may be wrong - but I think what you really want should look a lot like your arguments to qsub. So let say you have defined a job runner plugin called pbs_drmaa at the top of your job_conf.xml file. Then you could default everything to a single core by default and send big jobs to a destination with 8 cores with destinations and tool sections that look something like this... ... destinations default=singlecore destination id=singlecore runner=pbs_drmaa param id=native_specification-l nodes=1:ppn=1/param /destination destination id=multicore runner=pbs_drmaa param id=native_specification-l nodes=1:ppn=8/param /destination /destinations and ... tools tool id=bowtie2 destination=multicore / tool id=bowtie destination=multicore / tool id=deeptools destination=multicore / tool id=cufflinksdestination=multicore / tool id=cuffdiff destination=multicore / tool id=cuffmerge destination=multicore / tool id=tophat2 destination=multicore / /tools Again - that native specification could be wrong - probably best to test it out locally (or maybe Nate or JJ will step in and correct me). Hope this helps, -John On Mon, Jan 19, 2015 at 8:05 AM, Fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello gents, Once again I would like to convey my most sincere appreciation for your help!!! And yes I would like to hear your elaboration on my DRMAA runner which is what I'm using. So my installation looks like: galaxy -- pbs_drmaa -- torque Cordialement / Regards, Edgar Fernandez -Message d'origine- De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : January-18-15 8:59 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Galaxy generally defers to the DRM (torque in your case) for dealing with these things. In your job_conf.xml you can specify limits for memory or CPUs and Galaxy will pass these along to the DRM at which point it is up to the DRM to enforce these - details depend on if you are using the PBS runner or the DRMAA runner (let me know which and I can try to elobrate if that would be useful). In your particular case - I don't believe torque schedules RAM so things will generally only be... throttled... by CPUs counts. This is what I was told by the admins at MSI when I worked there anyway. If you want to place hard limits on RAM I think you need to upgrade to the MOAB scheduler or switch over to a different DRM entirely like SLURM. Even for DRMs that deal more directly with memory - Galaxy doesn't provide a general mechanism for passing this along to the tool (https://trello.com/c/3RkTDnIn) - so it would be up to the tool to interact with the environment variables your DRM sets . This sounds really terrible in the abstract - but it reality it usually isn't an issue - most of Galaxy's multi-core mappers say have relatively low memory per CPU usage - and for things like assemblers where this is more important - one can usually just assign them to their own CPU or something like that to ensure they get all the memory available. Unlike memory - Galaxy will attempt to pass the number of slots allocated to a job to the tools by setting the GALAXY_SLOTS environment variable. All of the
Re: [galaxy-dev] galaxy and torque - resource allocation
Hi Edgar, I'd suggest checking your Apache logs to see if the upload was denied by the server configuration (possibly for being too large). Also, please try using the modal upload method to see whether the upload is actually completing. This can be found by clicking the icon of a box with an up arrow at the top of the tool panel. There are multiple steps to an upload - the first is sending the data to the server. After that, Galaxy creates a job and detects metadata about the uploaded dataset. Prior to the modal upload, a (purple uploading) history item would be created as soon as the upload started, but if the transfer to the server was interrupted the history item may remain stuck in that state without providing feedback to the user that the upload was no longer progressing. The modal provides an upload progress bar, and only once all the data has been sent to the server does it create a history item (in the gray queued) state. On Thu, Jan 22, 2015 at 8:50 AM, Fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello John, This is totally excellent! This gave me a great idea for my little torque installation. I hope you don't mind but I have an unrelated issue with torque that I do not seem to grasp. My issue is that it take a rediculious amount of time to upload a 2Gb file. I tried many different configurations of apache to upload that 2Gb file without success. Galaxy keeps showing that arrow going up constantly (over 12h). And this is an upload from a file located on the server running galaxy. Here is some information from my installation. 1. Server redhat6 with galaxy behind an Apache HTTP Server proxy like described on your website. 2. I have Apache HTTP Server running as the galaxy user with a. Serving Galaxy at a sub directory b. Compression and caching c. Sending files using Apache You will see in attachment my apache's galaxy, deflate, expire and xsendfile configuration file. Furthermore, I've changed the following in galaxy.ini: apache_xsendfile = True upstream_gzip = False Any suggestions? Any information I missed? PLEASE HELP!!! Cordialement / Regards, Edgar Fernandez -Message d'origine- De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : January-21-15 9:34 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Was hoping someone with an actual torque cluster would respond. I think the way you would configure this might be for instance might be setting native_specification like -l nodes=1:ppn=n. Depending on how things are configured or simply because I am ignorant - this may be wrong - but I think what you really want should look a lot like your arguments to qsub. So let say you have defined a job runner plugin called pbs_drmaa at the top of your job_conf.xml file. Then you could default everything to a single core by default and send big jobs to a destination with 8 cores with destinations and tool sections that look something like this... ... destinations default=singlecore destination id=singlecore runner=pbs_drmaa param id=native_specification-l nodes=1:ppn=1/param /destination destination id=multicore runner=pbs_drmaa param id=native_specification-l nodes=1:ppn=8/param /destination /destinations and ... tools tool id=bowtie2 destination=multicore / tool id=bowtie destination=multicore / tool id=deeptools destination=multicore / tool id=cufflinksdestination=multicore / tool id=cuffdiff destination=multicore / tool id=cuffmerge destination=multicore / tool id=tophat2 destination=multicore / /tools Again - that native specification could be wrong - probably best to test it out locally (or maybe Nate or JJ will step in and correct me). Hope this helps, -John On Mon, Jan 19, 2015 at 8:05 AM, Fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello gents, Once again I would like to convey my most sincere appreciation for your help!!! And yes I would like to hear your elaboration on my DRMAA runner which is what I'm using. So my installation looks like: galaxy -- pbs_drmaa -- torque Cordialement / Regards, Edgar Fernandez -Message d'origine- De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : January-18-15 8:59 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Galaxy generally defers to the DRM (torque in your case) for dealing with these things. In your job_conf.xml you can specify limits for memory or CPUs and Galaxy will pass these along to the DRM at which point it is up to the DRM to enforce these - details depend on if you are using the PBS runner or the DRMAA runner (let me know which and I can try to elobrate if that would be useful). In your particular case - I don't believe torque
Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.
Thanks Peter. I see how this feature would be useful, but the program I'm writing a wrapper for has an argument with values corresponding to the input files. I am using a repeat tag to maintain this order. With the multi-run option, files are selected in a random manner and added to the job queue. It is best not to display the multi-run option in this case. I see there is a TODO on this already: https://bitbucket.org/galaxy/galaxy-dist/src/a2308bdc93b897af974766b190abe019ade49e9a/lib/galaxy/tools/parameters/basic.py?at=default#cl-2084 For now, I have set allow=False but I believe this is best set at the param tag level: param type=data multirun=false / Vimal On Wed, Jan 21, 2015 at 2:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote: I think this is the (relatively new) Galaxy ability to automatically run N copies of your tool given N input files, making N outputs and is related to the collections work. (This is possible if your tool takes a single input file) Peter On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan vi...@biotechcoder.com wrote: Hi all, I am trying to create a select box with the possibility of selecting only a single item from the input dataset (figure 1). This works fine but the option for selecting multiple files is still visible (figure 2). The multiple=false attribute has no effect. Figure: http://i.imgur.com/oJVFCoF.png I have the following in my XML. param format=tabular name=ribo_files type=data label=Select Ribo-Seq alignment file multiple=false /param Any suggestions? galaxy-dist revision 5f4c13d622b8 Regards, Vimalkumar Velayudhan ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy and torque - resource allocation
Hello Nate, Thank you for answer so quickly. My apache logs (/var/log/httpd/galaxy-prod-access_log) looks like this ip_addr - - [22/Jan/2015:10:17:31 -0500] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 37 ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 1401 ip_addr - - [22/Jan/2015:10:17:36 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:40 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:44 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:48 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 And my galaxy logs (/home/galaxy/galaxy-prod/config/main.log): ip_addr - - [22/Jan/2015:10:17:31 -0400] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] POST /galaxy-prod/tool_runner/index HTTP/1.1 500 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 Error - type 'exceptions.OverflowError': signed integer is greater than maximum ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 URL: http://esiservera.esi.umontreal.ca:8081/galaxy-prod/tool_runner/index File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 185 in handle_request kwargs = trans.request.params.mixed() File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 900 in params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 892 in str_params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 818 in str_POST File '/usr/lib64/python2.6/cgi.py', line 508 in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File '/usr/lib64/python2.6/cgi.py', line 635 in read_multi headers = rfc822.Message(self.fp) File '/usr/lib64/python2.6/rfc822.py', line 108 in __init__ self.readheaders() File '/usr/lib64/python2.6/rfc822.py', line 155 in readheaders line = self.fp.readline() File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py', line 482 in readline data = self.file.readline(max_read) File '/usr/lib64/python2.6/socket.py', line 415 in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum CGI Variables - CONTENT_LENGTH: '2625522525' CONTENT_TYPE: 'multipart/form-data; boundary=WebKitFormBoundary9c9hOVrAGAXKJtdd' HTTP_ACCEPT: '*/*' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=d122f4f53e5da72f16add67ded507460da12cda8c8b0781476c9ddbea84bd40a1e299b3d9b7a9e3a; galaxysession=d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e' HTTP_HOST: 'esiservera.esi.umontreal.ca:8081' HTTP_ORIGIN: 'http://esiservera.esi.umontreal.ca:8081' HTTP_REFERER: 'http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/tool_runner/index' REMOTE_ADDR: 'ip_addr' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy-prod' SERVER_NAME: 'esiservera.esi.umontreal.ca' SERVER_PORT: '7112' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -- application:
[galaxy-dev] show stopper for my galaxy installation
Hello gents, I started this new thread because I have a showstopper for my installation of galaxy. Here's my situation: 1. I have a galaxy server that has internet access. 2. My galaxy server is also my torque server and my only torque submit node. 3. I have three torque compute nodes that DOESN'T have internet access. Now, I've tried uploading a file (larger than 2Gb) via and URL and it fails. However, I've added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it works. Now, my compute nodes are in a network that is completely protected from the outside world. So no internet access. What are my option in this case? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] show stopper for my galaxy installation
The tool to fetch data isn't being run on your submit node but instead on the cluster, which is the problem. It's a fairly easy to solve problem: - In your job_conf you'll need to define a way to run jobs locally (either via local runner, or via a special queue dedicated to your submit node) - Then you'll need to specify that the upload tool is forced to that job runner. Something like this (untested, probably invalid xml... ) plugins workers=4 plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner / !-- your torque runner here -- /plugins destinations default=cluster destination id=local runner=local !-- your cluster dest here -- /destinations tools !-- we force the upload tool to the local job runner, thereby bypassing the issue of internet access on the cluster nodes -- tool id=upload1 destination=local / /tools Cheers, Eric 2015-01-22 13:51 GMT-06:00 Fernandez Edgar edgar.fernan...@umontreal.ca: Hello gents, I started this new thread because I have a showstopper for my installation of galaxy. Here’s my situation: 1. I have a galaxy server that has internet access. 2. My galaxy server is also my torque server and my only torque submit node. 3. I have three torque compute nodes that DOESN’T have internet access. Now, I’ve tried uploading a file (larger than 2Gb) via and URL and it *fails*. However, I’ve added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it *works*. Now, my compute nodes are in a network that is completely protected from the outside world. So no internet access. What are my option in this case? Cordialement / Regards, *Edgar Fernandez* System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication ( Bur. : *1-514-343-6111 poste 16568* *Université de Montréal* PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy and torque - resource allocation
Hi Edgar, Please make sure you have disabled the developer options `use_interactive` and `debug` in galaxy.ini, then restart your Galaxy server and try the upload again. Also, please try out the modal upload dialog as I suggested, it should prevent a stuck upload in the future. --nate On Thu, Jan 22, 2015 at 10:25 AM, Fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello Nate, Thank you for answer so quickly. My apache logs (/var/log/httpd/galaxy-prod-access_log) looks like this *ip_addr - - [22/Jan/2015:10:17:31 -0500] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 37* *ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235* *ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 1401* *ip_addr - - [22/Jan/2015:10:17:36 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235* *ip_addr - - [22/Jan/2015:10:17:40 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235* *ip_addr - - [22/Jan/2015:10:17:44 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235* *ip_addr - - [22/Jan/2015:10:17:48 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235* And my galaxy logs (/home/galaxy/galaxy-prod/config/main.log): ip_addr - - [22/Jan/2015:10:17:31 -0400] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] POST /galaxy-prod/tool_runner/index HTTP/1.1 500 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 Error - type 'exceptions.OverflowError': signed integer is greater than maximum ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 URL: http://esiservera.esi.umontreal.ca:8081/galaxy-prod/tool_runner/index File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 185 in handle_request kwargs = trans.request.params.mixed() File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 900 in params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 892 in str_params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 818 in str_POST File '/usr/lib64/python2.6/cgi.py', line 508 in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File '/usr/lib64/python2.6/cgi.py', line 635 in read_multi headers = rfc822.Message(self.fp) File '/usr/lib64/python2.6/rfc822.py', line 108 in __init__ self.readheaders() File '/usr/lib64/python2.6/rfc822.py', line 155 in readheaders line = self.fp.readline() File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py', line 482 in readline data = self.file.readline(max_read) File '/usr/lib64/python2.6/socket.py', line 415 in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum CGI Variables - CONTENT_LENGTH: '2625522525' CONTENT_TYPE: 'multipart/form-data; boundary=WebKitFormBoundary9c9hOVrAGAXKJtdd' HTTP_ACCEPT: '*/*' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=d122f4f53e5da72f16add67ded507460da12cda8c8b0781476c9ddbea84bd40a1e299b3d9b7a9e3a; galaxysession=d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e' HTTP_HOST: 'esiservera.esi.umontreal.ca:8081' HTTP_ORIGIN: 'http://esiservera.esi.umontreal.ca:8081'
Re: [galaxy-dev] galaxy and torque - resource allocation
Hello Nate, I just tried the modal upload dialog and it says File exceeds 2GB. Please use FTP client. Is there a way to increase that file size limitation? Cordialement / Regards, Edgar Fernandez De : Nate Coraor [mailto:n...@bx.psu.edu] Envoyé : January-22-15 12:02 PM À : Fernandez Edgar Cc : John Chilton; galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Hi Edgar, Please make sure you have disabled the developer options `use_interactive` and `debug` in galaxy.ini, then restart your Galaxy server and try the upload again. Also, please try out the modal upload dialog as I suggested, it should prevent a stuck upload in the future. --nate On Thu, Jan 22, 2015 at 10:25 AM, Fernandez Edgar edgar.fernan...@umontreal.camailto:edgar.fernan...@umontreal.ca wrote: Hello Nate, Thank you for answer so quickly. My apache logs (/var/log/httpd/galaxy-prod-access_log) looks like this ip_addr - - [22/Jan/2015:10:17:31 -0500] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 37 ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 1401 ip_addr - - [22/Jan/2015:10:17:36 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:40 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:44 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:48 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 And my galaxy logs (/home/galaxy/galaxy-prod/config/main.log): ip_addr - - [22/Jan/2015:10:17:31 -0400] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] POST /galaxy-prod/tool_runner/index HTTP/1.1 500 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 Error - type 'exceptions.OverflowError': signed integer is greater than maximum ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 URL: http://esiservera.esi.umontreal.ca:8081/galaxy-prod/tool_runner/index File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 185 in handle_request kwargs = trans.request.params.mixed() File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 900 in params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 892 in str_params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 818 in str_POST File '/usr/lib64/python2.6/cgi.py', line 508 in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File '/usr/lib64/python2.6/cgi.py', line 635 in read_multi headers = rfc822.Message(self.fp) File '/usr/lib64/python2.6/rfc822.py', line 108 in __init__ self.readheaders() File '/usr/lib64/python2.6/rfc822.py', line 155 in readheaders line = self.fp.readline() File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py', line 482 in readline data = self.file.readline(max_read) File '/usr/lib64/python2.6/socket.py', line 415 in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum CGI Variables - CONTENT_LENGTH: '2625522525tel:2625522525' CONTENT_TYPE: 'multipart/form-data; boundary=WebKitFormBoundary9c9hOVrAGAXKJtdd' HTTP_ACCEPT: '*/*' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_CONNECTION: 'Keep-Alive'
Re: [galaxy-dev] galaxy and torque - resource allocation
Hello guys, I want to apologies. I didn’t see the note: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator). and I forgot my file was that big. Please accept my sincere apologies. Cordialement / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : January-22-15 12:35 PM À : 'Nate Coraor' Cc : John Chilton; galaxy-...@bx.psu.edu Objet : RE: [galaxy-dev] galaxy and torque - resource allocation Hello Nate, I just tried the modal upload dialog and it says File exceeds 2GB. Please use FTP client. Is there a way to increase that file size limitation? Cordialement / Regards, Edgar Fernandez De : Nate Coraor [mailto:n...@bx.psu.edu] Envoyé : January-22-15 12:02 PM À : Fernandez Edgar Cc : John Chilton; galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Hi Edgar, Please make sure you have disabled the developer options `use_interactive` and `debug` in galaxy.ini, then restart your Galaxy server and try the upload again. Also, please try out the modal upload dialog as I suggested, it should prevent a stuck upload in the future. --nate On Thu, Jan 22, 2015 at 10:25 AM, Fernandez Edgar edgar.fernan...@umontreal.camailto:edgar.fernan...@umontreal.ca wrote: Hello Nate, Thank you for answer so quickly. My apache logs (/var/log/httpd/galaxy-prod-access_log) looks like this ip_addr - - [22/Jan/2015:10:17:31 -0500] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 37 ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:32 -0500] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 1401 ip_addr - - [22/Jan/2015:10:17:36 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:40 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:44 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 ip_addr - - [22/Jan/2015:10:17:48 -0500] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 235 And my galaxy logs (/home/galaxy/galaxy-prod/config/main.log): ip_addr - - [22/Jan/2015:10:17:31 -0400] POST /galaxy-prod/tool_runner/upload_async_create HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] POST /galaxy-prod/tool_runner/index HTTP/1.1 500 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 Error - type 'exceptions.OverflowError': signed integer is greater than maximum ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 ip_addr - - [22/Jan/2015:10:17:32 -0400] GET /galaxy-prod/tool_runner/upload_async_message HTTP/1.1 200 - http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36 URL: http://esiservera.esi.umontreal.ca:8081/galaxy-prod/tool_runner/index File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 185 in handle_request kwargs = trans.request.params.mixed() File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 900 in params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 892 in str_params File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 818 in str_POST File '/usr/lib64/python2.6/cgi.py', line 508 in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File '/usr/lib64/python2.6/cgi.py', line 635 in read_multi headers = rfc822.Message(self.fp) File '/usr/lib64/python2.6/rfc822.py', line 108 in __init__ self.readheaders() File '/usr/lib64/python2.6/rfc822.py', line 155 in readheaders line = self.fp.readline() File
Re: [galaxy-dev] Manually installing rsem_datatypes package from toolshed
Yup, that fixed it. Thanks! On Wed, Jan 21, 2015 at 6:51 PM, John Chilton jmchil...@gmail.com wrote: I believe this is an ancient bug that I has been fixed in Galaxy's central branch but is not in the latest release: https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 The previous workaround for this bug was that one would need to import the datatype at the top of registry.py (import rsem_datatypes) which is another option for addressing this problem instead of applying the patch. Hope this helps, -John On Wed, Jan 21, 2015 at 2:16 PM, Ryan G ngsbioinformat...@gmail.com wrote: I'm trying to manually install rsem_datatypes package into my local Galaxy install. I can't use the Toolshed for various reasons. Anyway, I downloaded the package using hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes I see two files: 1) datatypes_conf.xml, and 2) rsem.py I copied the datatype extension ... lines into my config/datatypes_conf.xml file. I also copied rsem.py to lib/galaxy/datatypes/. When I restart Galaxy, it doesn't seem that Galaxy knows how to handle rsem datatypes, as I get this error: galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' I'm obviously missing something but not sure what. I suspect maybe the rsem.py file is not in the right place? Ryan ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
