Re: [galaxy-dev] Local installation: Uploading fastq file takes ages - why?
Hi Nate, Thanks for your reply. Both debug and use_interactive are set to true in my universe_wsgi.ini. However, I discovered a short while after sending the message that uploading the gzipped files made the process very fast. Obviously it's a clear short sight on my part, sorry. Regards, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: Nate Coraor [n...@bx.psu.edu] Sent: Thursday, August 29, 2013 5:07 PM To: בעז שאנן Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Local installation: Uploading fastq file takes ages - why? On Aug 14, 2013, at 8:39 AM, Boaz Shaanan wrote: Hi, On my local galaxy installation (updated to the latest version yesterday), it takes ages (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from 132.72.88.186. Initially there is an error message (the attached file also includes the debug url at the end) and after a while the upload proceeds but takes very long time. Transferring the file by sftp between the two computers takes only seconds. Is there anytning wrong with my installation (i.e. something is not properly defined or something like this). Hi Boaz, Could you make sure that debug and use_interactive are both set to False in universe_wsgi.ini? Thanks, --nate I'd appreciate your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 galaxy_local_server_error.txt___ 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] Local installation: Uploading fastq file takes ages - why?
On Aug 14, 2013, at 8:39 AM, Boaz Shaanan wrote: Hi, On my local galaxy installation (updated to the latest version yesterday), it takes ages (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from 132.72.88.186. Initially there is an error message (the attached file also includes the debug url at the end) and after a while the upload proceeds but takes very long time. Transferring the file by sftp between the two computers takes only seconds. Is there anytning wrong with my installation (i.e. something is not properly defined or something like this). Hi Boaz, Could you make sure that debug and use_interactive are both set to False in universe_wsgi.ini? Thanks, --nate I'd appreciate your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 galaxy_local_server_error.txt___ 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/
[galaxy-dev] Local installation: Uploading fastq file takes ages - why?
Hi, On my local galaxy installation (updated to the latest version yesterday), it takes ages (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from 132.72.88.186. Initially there is an error message (the attached file also includes the debug url at the end) and after a while the upload proceeds but takes very long time. Transferring the file by sftp between the two computers takes only seconds. Is there anytning wrong with my installation (i.e. something is not properly defined or something like this). I'd appreciate your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 /home/bshaanan/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 132.72.88.186 - - [14/Aug/2013:13:32:45 +0300] GET / HTTP/1.1 200 - - Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:32:52 +0300] GET /root/welcome HTTP/1.1 302 - http://dylan.bgu.ac.il:8082/; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:32:52 +0300] GET /history HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:32:58 +0300] GET /history/get_display_application_links HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/history; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:33:18 +0300] GET /user/login HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:33:29 +0300] POST /user/login?use_panels=False HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/user/login; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 /home/bshaanan/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927: SAWarning: The IN-predicate on request_type.id was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 132.72.88.186 - - [14/Aug/2013:13:33:30 +0300] GET / HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/user/login?use_panels=False; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:33:30 +0300] GET /root/welcome HTTP/1.1 302 - http://dylan.bgu.ac.il:8082/; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:33:30 +0300] GET /history HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:33:31 +0300] GET /history/get_display_application_links HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/history; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - - [14/Aug/2013:13:34:23 +0300] GET /tool_runner?tool_id=upload1 HTTP/1.1 200 - http://dylan.bgu.ac.il:8082/; Mozilla/5.0 (X11; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 132.72.88.186 - -
