Re: [galaxy-dev] Welcome.html page
On 03/09/2012 01:04 AM, Huayan Gao wrote: Dear Hans, I emptied cache and it is not showing up the changes. I changed a computer and tried again. No luck. Yes, I killed the process and restart the server, no luck. It should be pretty straight forward but it just did not come out as I expected. Any ideas? first (wild) guess: you have two galaxy servers (ie galaxy directories). you change the file in one, but in the web browser, you are looking at a different installation. so just double checking: what happens when you delete (ie re-name or move to a different location): ~/galaxy_dist/static/welcome.html ~/galaxy_dist/tool_conf.xml ~/galaxy_dist/tool_conf.xml.sample and restart the server? the missing tool_conf.xml should cause the start-up to fail Regards, Hans Best, Huayan On 8 Mar, 2012, at 10:52 PM, Hans-Rudolf Hotz wrote: Hi Huayan I got a silly question for you. My galaxy is running now but I'd like to customize it. I've changed the welcome.html page but the galaxy mirror site is showing the old one. Do I need to change some other files or other configurations? Are you sure the page is not cached locally? Also, I addlable in tool_conf.xml file but it does not show up either. Is there another file I need to change too? I assume you mean label, have you restarted your galaxy server? I hope this helps Regards, Hans Best, Huayan ___ 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/
[galaxy-dev] Tool and dynamic options
Hi everyone. I'm writing a tool that can take a parameter with a dynamic list of values. The tool XML file looks like this: conditional ... param name=outer type=select option value=1XYZ/option option value=2ZYX/option option value=3ZXY/option /param when value=1 param name=inner type=select ... /param /when /conditional I would like to generate the inner option elements dynamically by calling an external utility in response to the first parameter (outer), or at least some piece of python code. I know I can use options to load this from an external file, but that's not enough. I tried to use code, but I'm afraid I wasn't able to generate the list of options dynamically (by using the first conditional when selected). I couldn't find a tool that uses code to this end. Does anybody have any suggestion? I was thinking of adding a new attribute to options, like options load_from_command=. Would you accept such a patch to galaxy? Thanks. ___ 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] Display galaxy variable
Hello,
In a Galaxy tool, I would like to display a pre-completed path in the
xml inputbox, inside the tool.xml file.
Consequently, I would like to add a variable in an param value= /
tag , like this :
tool id=test name=test version=
command interpreter=shtest.sh $in $out/command
inputs
param name=filepath type=text size=100 value=/work/$out /
/inputs
...
and in test.sh : $out is defined to be ${trans.user.username}
Do you have any idea to display ${trans.user.username} variable in
order to be shown in galaxy interface (gui) thanks to xml file ?
I achieve to display ${trans.user.username} in
/templates/root/tool_menu.mako but not in the xml file.
Thanks in advance,
Sarah
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[galaxy-dev] Production environment and Apache's sendfile
Hi everyone. I've set up a galaxy production environment and it seems to be working. I've identified a couple of issues though: If I enable apache_xsendfile, the little eye icon (Display data in browser) on each dataset stops working. I get the following instead: The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this server My document root is not the same as the galaxy root (as suggested). Everything else seems to work. Is this a bug? Second question: I want to rotate the galaxy log file (as specified with paster.py serve --log-file. I can't find a way to reopen the logfile in galaxy without taking down the whole service, or a way to redirect the log to a pipe together while using --daemon. I cannot let the file grow forever. Any suggestions? Right now I've setup logrotate to copytruncate the log (the log is opened in append anyway), but it's not a very nice solution. Does paster support some standard signal such as SIGUSR1 to re-open log files? Thanks. ___ 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] postgres
Hi, thanks for the answer. I have one more question. Is there one main table (in the database), which creates one key for one job and this key is allocated over other tables? Thank you! Best, Christin Am 08.03.2012 16:40, schrieb Björn Grüning: Hi Christin, I would like to clarify whether we have understood something about the database correctly. Is is right that all calculations with galaxy are stored as a link in the database. And the data are stored somewhereelse? Yes, kind of :) Is it possible to store the data only in the database? No and its advisable to do so. Galaxy operates on files and they can be huge. It does not make much sense to store such data in a database. Best, Bjoern For some advice, I am very grateful. Best regards, Christin -- Christin Weinberg Institute for Applied Computer Science (IACS) FH Stralsund - University of Applied Sciences Phone: +49 3831 456948 E-Mail : christin.weinb...@fh-stralsund.de ___ 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] postgres
Yes, see the table 'job'. You may or may not find this helpful, but here's a big database schema from our wiki: http://wiki.g2.bx.psu.edu/DataModel?action=AttachFiledo=viewtarget=galaxy_schema.png -Dannon On Mar 9, 2012, at 8:00 AM, christin weinberg wrote: Hi, thanks for the answer. I have one more question. Is there one main table (in the database), which creates one key for one job and this key is allocated over other tables? Thank you! Best, Christin Am 08.03.2012 16:40, schrieb Björn Grüning: Hi Christin, I would like to clarify whether we have understood something about the database correctly. Is is right that all calculations with galaxy are stored as a link in the database. And the data are stored somewhereelse? Yes, kind of :) Is it possible to store the data only in the database? No and its advisable to do so. Galaxy operates on files and they can be huge. It does not make much sense to store such data in a database. Best, Bjoern For some advice, I am very grateful. Best regards, Christin -- Christin Weinberg Institute for Applied Computer Science (IACS) FH Stralsund - University of Applied Sciences Phone: +49 3831 456948 E-Mail : christin.weinb...@fh-stralsund.de ___ 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/
[galaxy-dev] How to configure Get Data | get microbial data
Dear all, I have spent several days trying to make get microbial data to work in my local Galaxy instance, but failed. What i did is: 1. cd /galaxy-dist/tool-data/ 2. nano microbial_data 3. uncomment the lines starting with ORG, CHR or DATA After that, i restarted Galaxy and can see the options on the web. However, it cannot work yet. I am pretty sure that is because the URLs are not properly specified and i don't have a local mirror of all the related files yet. Can anyone help and tell me where and how to download the files? And how can i continue to make it work? (In addition, i find some information under the link http://gmod.827538.n3.nabble.com/Setting-up-microbial-data-loc-given-a-mirror-of-NCBI-FTP-site-td2120728.html#a2122753. But still cannot figure out how to do it) THANKS A LOT!!! Cheers, Tyler ___ 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] Error when installing toolshed tool
I'm getting this error when I try to install the NGS Java toolkit toolshed...Version information for the tools included in the java_genomics_toolkit repository is missing. Reset all of this repository's metadata in the tool shed, then set the installed tool versions from the installed repository's Repository Actions menu. Installed 1 repository and all tools were loaded into tool panel section NGS: Toolkit:Installed repositories: java_genomics_toolkit.Any idea why the version number stuff is not correctly inserted in the database?Bug?ThanksThon ___ 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/
