[galaxy-dev] Jobs waiting in job queue
Hi Galaxy team, This is going to be a very unhelpful message but I hope you have some ideas to point me in the right direction! For some reason our local Galaxy instance (set up with the production server guide on the wiki minus all the fancy cluster stuff) is refusing to run jobs except after a restart. So we wish to execute our particular tool, it shows up in the history as grey and will remain that way. I have investigated all the logs and there are no error messages and for some reason the handler is not receiving the message to execute the tool. Once we reset Galaxy as soon as it has gone through its initial start-up process it executes our tool we wanted it to with no problems. We are operating with the latest version of galaxy-dist as of 30/07/12. I have investigated the web and manager logs as well as my apache logs just in case and have come up short. Any tips or ideas would be much appreciated! Cheers, Ed Department of Biochemistry, University of Otago, Dunedin, New Zealand. ___ 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] GFF tools
Hello, When I use one of GFF tool ( Filter GFF data by attribute http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filter_by_attribute using simple expressions OR Filter GFF data by feature count http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filter_by_feature_count using simple expressions OR Filter GTF data by attribute values_list http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gtf_filter_by_attribute_values_list) , I have this message : Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/filters/gff/gff_filter_by_attribute.py, line 55, in module attribute_types = from_json_string( sys.argv[4] ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py, line 384, in loads File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 402, in decode File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 420, in raw_decode simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) Could you please help me ? Thanks in advance, Sarah Maman ___ 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] Upload local files
Hi devs, when using the upload tool it would be nice to let the user specify paths to files stored on our internal servers like the admin can when choosing to add data to a library. Also it would be nice to be able to link to these files. Unfortunately I was not able to find the tool for uploading files into a library so it would be nice if you can give me a hint. With this information I should be able to extend the normal upload tool. Thanks in advance! Cheers, Sascha Kastens Project Manager GATC Biotech AG Jakob-Stadler-Platz 7 D-78467 Konstanz Phone: +49 (0) 7531-81604110 Fax: +49 (0) 7531-816081 Email: s.kast...@gatc-biotech.com http://www.gatc-biotech.com http://www.twitter.com/gatcbiotech http://www.facebook.com/gatcbiotech http://www.xing.com/companies/gatcbiotechag GATC Biotech AG Chairman Supervisory Board: Fritz Pohl Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter. ___ 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] Old tool not showing up properly in Tool Shed
Hi all, I've just uploaded an update to my (previously protein only) sequence analysis bundle on the ToolShed, which is stuck with the original name: tmhmm_and_signalp This now offers Galaxy wrappers for several standalone command line sequence analysis tools: * SignalP 3.0 predicts signal peptides, see: http://www.cbs.dtu.dk/services/SignalP/ * TMHMM 2.0 predicts transmembrane helices, see: http://www.cbs.dtu.dk/services/TMHMM/ * Promoter 2.0 predicts eukaryotic PolII promoters [NEW WRAPPER], see: http://www.cbs.dtu.dk/services/Promoter/ * WoLF PSORT predicts Eukaryote protein sub-cellular localization, see: http://wolfpsort.org/ * Oomycete RXLR motif prediction - a Python script implementing three published methods, which calls SignalP 3.0 and HMMER 2.3.2 internally. In this update I added the new Promoter 2.0 wrapper, and made some small changes to the SignalP and TMHMM wrappers. The other tools are unchanged. Looking at the tool bundle via the Tool Shed, for revision 7:9b45a8743100 it only shows four valid tools: * Promoter 2.0 - Find eukaryotic PolII promoters in DNA sequences * RXLR Motifs - Find RXLR Effectors of Plant Pathogenic Oomycetes * SignalP 3.0 - Find signal peptides in protein sequences * TMHMM 2.0 - Find transmembrane domains in protein sequences Why is this missing?: * WoLF PSORT - Eukaryote protein subcellular localization prediction The missing tool is NOT showing up under Browse my invalid tools, and the wrapper XML seems to still be there if I browse the tip files. Thanks, 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/
Re: [galaxy-dev] Old tool not showing up properly in Tool Shed
Hi Peter, This issue is part of a larger known issue that I have not had time to resolve due to preparation for the 2 consecutive recent conferences I've been involved in. This is my next chunk of though, and I'll let you know when I get it finished. In the meantime, even though the WoLF PSORT tool is not being displayed as part of what will get installed, it should still be installed along with the tools that are being displayed. Greg Von Kuster On Jul 30, 2012, at 10:37 AM, Peter Cock wrote: Why is this missing?: * WoLF PSORT - Eukaryote protein subcellular localization prediction The missing tool is NOT showing up under Browse my invalid tools, and the wrapper XML seems to still be there if I browse the tip files. Thanks, 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/ ___ 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] Old tool not showing up properly in Tool Shed
On Mon, Jul 30, 2012 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, This issue is part of a larger known issue that I have not had time to resolve due to preparation for the 2 consecutive recent conferences I've been involved in. This is my next chunk of though, and I'll let you know when I get it finished. In the meantime, even though the WoLF PSORT tool is not being displayed as part of what will get installed, it should still be installed along with the tools that are being displayed. Greg Von Kuster Thanks Greg - good to know you've already got a handle on what is amiss here. 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/
Re: [galaxy-dev] GFF tools
When I use one of GFF tool ( Filter GFF data by attribute using simple expressions OR Filter GFF data by feature count using simple expressions OR Filter GTF data by attribute values_list) , I have this message : Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/filters/gff/gff_filter_by_attribute.py, line 55, in module attribute_types = from_json_string( sys.argv[4] ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py, line 384, in loads File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 402, in decode File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 420, in raw_decode simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) A couple questions: Are you seeing this problem on a local instance or on our public server? Is it happening for all GFF/GTF datasets or just some? Thanks, 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/
Re: [galaxy-dev] bcftools
Hello HK, This tool and the others related to VCF format that are on Test only or on Main as beta are currently under development. Thank you for your patience while we catch up on replies, last week was very busy for our team (GCC 2012), Jen Galaxy team On 7/24/12 7:23 AM, Hongkyun Kim wrote: Dear all, I am not sure whether the following issue is related to development or bug report. In main galaxy website, I generated bcf files using mpileup, and now would like to convert bcf files to vcf files. However, I cannot find this conversion tool. Oddly, I find this tool in test galaxy website. Is this bug or in the process of the development? Thank you, HK ___ 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/ -- Jennifer Jackson http://galaxyproject.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/
[galaxy-dev] PBS Server Throwing Errors
Hi, Galaxy Community, Greetings from The University of Chicago; I hope all who attended the Galaxy conference enjoyed it as much as I did. I have searched the mailing list archives as well as Google to a resolve problem I am seeing, however I am somewhat at a loss as to the next course of action I should be taking to bring this issue to a close. I am hoping that one of the bright minds on this mailing list could help me shed some light on the solution to my problem, or at least help me identify a root cause. I have configured Galaxy to integrate with TORQUE (version 4.0.2) server, and successfully built the PBS python egg as specified in the Galaxy documentation. I am using Python version 2.6 and the latest build of Galaxy. Whenever I launch a job from the Galaxy UI, I get the following error message(s) on the PBS server: 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=AlternateUserAuthentication, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=QueueJob, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=Disconnect, from galaxy@ 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server Version = 4.0.2, loglevel = 1 One thing I did notice, that suggests there might be a problem, is that there is no hostname after the galaxy@; most of the other messages in this log file have a host name appended to log entry, i.e.: 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request received from root@sc01, sock=10 I have completed a tcpdump on the schedule node, and I can definitely see bi-directional traffic between the Galaxy server and the scheduler node on TCP port 15001. In addition to this, I have installed the TORQUE client tools on on the Galaxy server, and can spawn an interactive job with qsub -I, as well as check the status of queued jobs using qstat (from the Galaxy server). This suggests to me that there a potential problem with the PBS Egg, although I am not certain. Has anybody seen something like this before, or could somebody point me in the right direction? We do have a support contract with Adaptive Computing, and I am opening a ticket with them as well, however I wanted to reach out to the Galaxy community to cover all of my bases. Thank-you so much for taking the time to read my email. Dan Sullivan ___ 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] Upload local files
Yes, we'd like to do this as well. Our users data are all on the servers, not on their Windows PCs and requiring the admin create shared data libraries is an overhead we'd rather avoid. Thanx, Russell Smithies Infrastructure Technician T 03 489 9085 M 027 4734 600 E russell.smith...@agresearch.co.nz Invermay Agricultural Centre Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand T +64 3 489 3809 F +64 3 489 3739 www.agresearch.co.nzhttp://www.agresearch.co.nz/ From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Sascha Kastens Sent: Tuesday, 31 July 2012 2:09 a.m. To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload local files Hi devs, when using the upload tool it would be nice to let the user specify paths to files stored on our internal servers like the admin can when choosing to add data to a library. Also it would be nice to be able to link to these files. Unfortunately I was not able to find the tool for uploading files into a library so it would be nice if you can give me a hint. With this information I should be able to extend the normal upload tool. Thanks in advance! Cheers, Sascha Kastens Project Manager GATC Biotech AG Jakob-Stadler-Platz 7 D-78467 Konstanz Phone: +49 (0) 7531-81604110 Fax: +49 (0) 7531-816081 Email: s.kast...@gatc-biotech.commailto:s.kast...@gatc-biotech.com http://www.gatc-biotech.com http://www.twitter.com/gatcbiotech http://www.facebook.com/gatcbiotech http://www.xing.com/companies/gatcbiotechag GATC Biotech AG Chairman Supervisory Board: Fritz Pohl Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter. === Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. === ___ 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/
