Re: [galaxy-dev] Server error from history view
Hi Isabelle, thank you for your help. However filter-with=gzip is disabled in our configuration. I set everything according to the guide on https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer. The gzip option you see in my log is from the Apache server. Sarah On 03/10/2011 07:08 PM, Isabelle Phan wrote: Hello Sarah, (my galaxy-dev account is broken, read your post on nabble) You need to disable filter-with=gzip in order to set debug=False But in any case, I have not seen a difference in the log, so my take is that galaxy only ever runs in debug mode. Isabelle ___ 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] Upload files from filesystem paths - backwards checkboxes
On Thu, Mar 10, 2011 at 5:53 PM, Glen Beane glen.be...@jax.org wrote: On Mar 10, 2011, at 12:24 PM, Peter Cock wrote: Hi all, Via the Galaxy admin interface, I'm currently importing some BAM files into a library from the local file system. Since they are big, I don't want Galaxy to copy them. So I looked at the Copy data into Galaxy? option and made sure it wasn't ticked. Galaxy did copy the file :( I looked at the interface again, and see you have: Copy data into Galaxy? [check box] No Normally data uploaded with this tool is copied into Galaxy's files directory so any later changes to the data will not affect Galaxy. However, this may not be desired (especially for large NGS datasets), so use of this option will force Galaxy to always read the data from its original path. You've got a tick box labelled No so it does the opposite to the question above it. That is a HORRIBLE interface. I can't be the first person to be tricked by it, can I? I had a co-worker mess this up too. I thought this was a poor design decision. I thought maybe yes/no radio options would work. Copy data into galaxy? yes(*) no( ) I would urge you to remove the work No and flip the meaning (and default) to match. But that could confuse existing admin users used to clicking from previous habit. How about making it a select parameter instead, with options Copy files (default) and Link to files which is very explicit? I think this would be better than the current no check box, and more explicit than my yes(*) no () radio buttons You may be right, but switching from a checkbox to a select isn't as easy as it could be... at least not with my familiarity with the code base. Likewise for the Preserve directory structure? setting, I'd remove the No caption and flip the setting, or just replace the backwards tick box with a select parameter offering Preserve directory structure and Place in selected folder (or something like that). Pretty please? How about if I write and test the patch? Patch for flipping the Preserve directory structure? setting, which I hope you can test then merge/transplant to the trunk: https://bitbucket.org/peterjc/galaxy-central/changeset/669dcc2803ba I'm still working on the Copy data into Galaxy? setting... 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] NoneType dereference on the jobs view
Hello Ry4an, Thanks for the patch - it's been applied in change set 5214:0b9bba943c8f. Greg Von Kuster On Mar 10, 2011, at 6:15 PM, Ry4an Brase wrote: Intermittently, and always during periods of high load we'll get a 500 Server error from the Admin 'Manage Jobs' list. In the logs the stacktrace looks like: http://paste.pocoo.org/show/351374/ Attached is the patch JJ provided to work around jobs without histories, but I thought I'd bring it up here too in case either others are seeing it or someone knows a root cause. Thanks! -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu job-history-none.patch___ 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/ Greg Von Kuster Galaxy Development Team g...@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] inputs sanitization...
Hi Kostas,
look in ~/lib/galaxy/util/__init__.py:
# characters that are allowed but need to be escaped
mapped_chars = { '' :'__gt__',
'' :'__lt__',
' :'__sq__',
'' :'__dq__',
'[' :'__ob__',
']' :'__cb__',
'{' :'__oc__',
'}' :'__cc__',
'@' : '__at__',
'\n' : '__cn__',
'\r' : '__cr__',
'\t' : '__tc__'
}
On Mar 11, 2011, at 6:11 AM, Kostas Karasavvas wrote:
Hi all!
I found the following in the mailing list archives. Does anyone know
where I can find a complete list of the sanitization taking place?
'' __gt__
'@' __at__
etc.
Thank you,
Kostas
It's worth noting that command line parameters are sanitized for
security purposes, so passing them unsanitized should only be done in
controlled environments where security is not a concern. Otherwise,
parameters should be restored to their original values by the tool or
a wrapper around the tool.
--nate
On Oct 5, 2010, at 10:10, Jelle Scholtalbers j.scholtalbers at
gmail.com wrote:
Hi,
take a look at options sanitize=False / as used also in
tools/fastq/fastq_manipulation.xml
Cheers,
Jelle
On Tue, Oct 5, 2010 at 12:39 AM, Zhe Chen zhe at lanl.gov wrote:
Hi,
I was implementing a galaxy tool. A problem occurs when my input contains
, linebreak, galaxy seems traslate them to __gt__, __crcn__. Is
there a way to stop this translation?
Or suggestion to fix this problem?
Thanks
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Greg Von Kuster
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g...@bx.psu.edu
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Re: [galaxy-dev] Upload files from filesystem paths - backwards checkboxes
Hello Peter, Thanks for the patch - I've applied a corrected version of it in change set 5215:74c4dd43485a. Let me know if you'd rather have me flip the Copy data into Galaxy? feature. I'd be happy to, but I don't want to reinvent the wheel if you're close. Thanks! Greg Von Kuster On Mar 11, 2011, at 7:31 AM, Peter Cock wrote: Patch for flipping the Preserve directory structure? setting, which I hope you can test then merge/transplant to the trunk: https://bitbucket.org/peterjc/galaxy-central/changeset/669dcc2803ba I'm still working on the Copy data into Galaxy? setting... Greg Von Kuster Galaxy Development Team g...@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] Upload files from filesystem paths - backwards checkboxes
On Fri, Mar 11, 2011 at 3:04 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Thanks for the patch - I've applied a corrected version of it in change set 5215:74c4dd43485a. Let me know if you'd rather have me flip the Copy data into Galaxy? feature. I'd be happy to, but I don't want to reinvent the wheel if you're close. Thanks! Greg Von Kuster Using util.string_as_bool looks good - I didn't know about that and it looks far more rhobust. Would you might doing Copy data into Galaxy? as well? I got most of the way but got dragged off to a meeting in the middle. 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/
[galaxy-dev] Connecting Galaxy to multiple Remote Clusters?
Hello, I've read through past emails that connecting Galaxy to a remote cluster is possible but I wanted to ask if it was possible to setup Galaxy as a standalone webserver and have it use multiple remote clusters (multiple head nodes each with their own compute nodes) and if so what the best strategy to implement this is? Also on one of these clusters we are not able to mount an NFS directory onto the compute nodes, since we do not own/manage it. Your help is greatly appreciated. Thanks, Joe ___ 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] Login problem.
Dear Galaxy development team, I've got a problem using the login function of Galaxy. So I downloaded a copy of Galaxy distribution and installed it on a local machine, then I installed PostgreSQL on this machine and made the necessary changes to the universe_wsgi.ini file and Galaxy is able to the use the PostgreSQL database to store information. I was able to register a user account and then I could login to the system for the first time, but after I logout and login again, the system always says that I am logged out. I checked the log file of Postgresql and the log file of Galaxy system, there is no error message indicating what happened at all. I restarted Postgresql database and Galaxy system and then I was able to login, but after I logged out, I can not login again! Have you guys met this kind of problem before? Any suggestions on what could be the cause of this problem? Thanks so much! Luobin ___ 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 files from filesystem paths - backwards checkboxes
Hi Peter, This has been resolved in change set 5217:70d7d0bfaad6, where I've changed the check box into a select list per your suggestion. Thanks! Greg Von Kuster On Mar 10, 2011, at 12:24 PM, Peter Cock wrote: Hi all, Via the Galaxy admin interface, I'm currently importing some BAM files into a library from the local file system. Since they are big, I don't want Galaxy to copy them. So I looked at the Copy data into Galaxy? option and made sure it wasn't ticked. Galaxy did copy the file :( I looked at the interface again, and see you have: Copy data into Galaxy? [check box] No Normally data uploaded with this tool is copied into Galaxy's files directory so any later changes to the data will not affect Galaxy. However, this may not be desired (especially for large NGS datasets), so use of this option will force Galaxy to always read the data from its original path. You've got a tick box labelled No so it does the opposite to the question above it. That is a HORRIBLE interface. I can't be the first person to be tricked by it, can I? I would urge you to remove the work No and flip the meaning (and default) to match. But that could confuse existing admin users used to clicking from previous habit. How about making it a select parameter instead, with options Copy files (default) and Link to files which is very explicit? Likewise for the Preserve directory structure? setting, I'd remove the No caption and flip the setting, or just replace the backwards tick box with a select parameter offering Preserve directory structure and Place in selected folder (or something like that). Pretty please? How about if I write and test the patch? 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/ Greg Von Kuster Galaxy Development Team g...@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/
