Re: [galaxy-dev] FastQC files are not being recognized by
Try the fastqsanger datatype if it works fine if not try the others such as fastqillumina etc Thanks Ambrose -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ricardo Perez Sent: 18 July 2013 20:41 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] FastQC files are not being recognized by Dear all, We are doing some processes in our server that use fastq files. We have obtained the data in .sra format and then convert them into fastq format using the sra tool kit. However, when we upload this files into galaxy, some tools does not recognize the file as fastq. When we apply FasQC:Read QC, under summary statistics it says that encoding is Sanger / Illumina 1.9. Is this an error of our part while installing galaxy in our server? Thank you for your time, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. ___ 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] Strange behaviour with galaxy history
Many thanks for the observation. This will come handy next time I hit the same rock. I hope not so soon. Ambrose -Original Message- From: Groot, Philip de [mailto:philip.degr...@wur.nl] Sent: 16 July 2013 12:03 To: Carl Eberhard Cc: galaxy-dev@lists.bx.psu.edu; Ambrose Andongabo (RRes-Roth) Subject: RE: Strange behaviour with galaxy history Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ From: Carl Eberhard [carlfeberh...@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; ambrose.andong...@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nlmailto:philip.degr...@wur.nl wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786tel:%2B31-317-485786 F: +31-317-483342tel:%2B31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nlhttp://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus
Re: [galaxy-dev] [Galaxy-gcc2013] Strange behaviour with galaxy history
Dear Carl, The javascript console displayed no errors. Below is the output of hg summary [root@vnc galaxy-dist]# hg summary not trusting file /home/data/galaxy-python/galaxy-dist/.hg/hgrc from untrusted user andongab, group csys not trusting file /home/data/galaxy-python/galaxy-dist/.hg/hgrc from untrusted user andongab, group csys parent: 10002:9d42f1e32efb For user impersonation, fully log the admin out prior to assuming user persona to avoid any history/session corruption. branch: stable commit: 241 unknown (clean) update: (current) As for the galaxy log, there is no error 149.155.13.62 - - [02/Jul/2013:15:40:33 +0100] GET /api/histories/2d89e36a8c9b5508 HTTP/1.1 200 - http://vnc:8080/history; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 149.155.13.62 - - [02/Jul/2013:15:40:37 +0100] GET /api/histories/2d89e36a8c9b5508 HTTP/1.1 200 - http://vnc:8080/history; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 149.155.13.62 - - [02/Jul/2013:15:40:42 +0100] GET /api/histories/2d89e36a8c9b5508 HTTP/1.1 200 - http://vnc:8080/history; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0 I hope this helps Thanks Ambrose From: Carl Eberhard [mailto:carlfeberh...@gmail.com] Sent: 02 July 2013 15:33 To: Ambrose Andongabo (RRes-Roth) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [Galaxy-gcc2013] Strange behaviour with galaxy history Hi, Ambrose A couple of places to start: Did the javascript console (in Firefox: Tools-Web Developer-Web Console) display any errors when you reloaded the failing saved history page? What does is the output of 'hg summary' when run in a terminal from your Galaxy root directory? I believe you mentioned there were no 'ERROR' messages in the Galaxy log; is this correct? Thanks for the report. (I'm moving this to the galaxy-dev mailing list). Carl On Tue, Jul 2, 2013 at 3:50 PM, Ambrose Andongabo (RRes-Roth) ambrose.andong...@rothamsted.ac.ukmailto:ambrose.andong...@rothamsted.ac.uk wrote: Dear All, I updated my local galaxy instance yesterday and all my users cannot access their saved histories. When they click on saved histories all they get is an empty page. Checking the database, all the histories are there. I cleared the browser cache as many suggested but no luck yet. Any ideas of what can be done?? Thanks Ambrose -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. ___ Galaxy-gcc2013 mailing list galaxy-gcc2...@lists.bx.psu.edumailto:galaxy-gcc2...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-gcc2013 -- This message has been scanned for viruses and dangerous content by MailScannerhttp://www.mailscanner.info/, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. ___ 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/
