- galaxy-dev - lists.galaxyproject.org

http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway
by Peter Cock 25 May '12

25 May '12

Hi, Could someone take a look at the Tool Shed server please? I'm getting this for http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway nginx/1.1.4 Thanks, Peter

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How must I configure Apache ?
by julie dubois 25 May '12

25 May '12

Hi, First, Sorry but, I'm a newbie with Apache and my questions will certainly appear stupid. To configure apache2, I've followed this wiki : http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy And I write these instructions : <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> RewriteEngine on <Location "/"> # Define the authentication method AuthType Basic AuthName Galaxy AuthUserFile /home/nate/htpasswd Require valid-user # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e </Location> RewriteRule ^/static/style/(.*) /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] </Location> But several problems appeared when I launched my Galaxy. First, must this instructions block be in the file apache2.conf or in the file default of sites-available directory ? If it must be in the file default, is it between the <VirtualHost> tags or out of these tags ? Second, I've created an htpaswd file in my home directory, but when I launch galaxy, it doesn't request me a login and password but it says me that Galaxy requires an user authentification and it must be an error in my apache configuration. Is it a problem with the instructions or with their place in configuration file ? Third the line </Location> appears two times in your instructions but it's wrong for apache. I've deleted the first but I'm note sure that Rewrite instructions must be in the <Location> block. And finally, I want to work with severals web processes and I want to add this configuration lines : <Proxy balancer://galaxy> ... </Proxy> Must I add to previous lines and where ? or Must I replace certain lines of previous block and if yes : which lines ? Thank you very much. Julie

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Files uploaded via FTP
by Sergei Manakov 24 May '12

24 May '12

Hello, There is an option of FTP upload on public galaxy, but my local galaxy lacks this capability. Is there a way to configure FTP upload for local galaxy? thanks, Sergei -- Sergei (Siarhei Manakou) Manakov California Institute of Technology +1 626 395 3593

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Trackster
by Xu, Jianpeng 24 May '12

24 May '12

Hi, I am trying to install the Trackster on the local galaxy. I read the webpage http://wiki.g2.bx.psu.edu/Learn/Visualization For example, to enable visualization of hg18, a file called hg18.len must exist in the previously specified folder. The contents of the .len file is tab-delimited and specifies the length of each chrom/contig of that build, each on a separate line, eg: chr1 27473282 chr2 38882233 ... chrX 28883322 My question is that : where to find the length information for chromosomes of hg18 ? Thanks, ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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About Galaxy Configuration
by Ciara Ledero 24 May '12

24 May '12

Hi there, I understand that everytime I create a new tool, I would have to restart Galaxy to see the changes that I've made. But if somebody else has already started Galaxy on our server, I won't be able to see my newly developed tool. I would be able to access the site, yes, but I won't see my tool. Is there a way around this? Cheers, CL

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Integrating Galaxy with JIRA for auto-ticket opening upon report
by Ann Black-Ziegelbein 24 May '12

24 May '12

Hi - We have integrated our local galaxy with JIRA such that when problems are reported through the galaxy interface, a problem ticket is automatically opened up. I had to make very minor changes to Galaxy in support of this, and I am contributing back my changes in this email in hopes they can be integrated in. What I changed: 1) config.py - support of a new config parm : error_email_from 2) dataset.py report_error - to use the new from email address if specified. 3) added in the new config parm to my universe_wsgi.* files error_email_to = jira-galaxy@blah error_email_from = galaxy-admin@blah I am attaching a zipper of the code changes. Thanks, Ann

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strange issues with tool list
by Sarah Diehl 24 May '12

24 May '12

Hi all, currently I face some strange behaviour of the tool panel in Galaxy if I add top-level label tags to the tool_conf.xml. The problem is that the labels stay forever, even if I remove them again from the tool_conf.xml and they also appear three section earlier than where I put them. I tried to remove all tool configs except the one tool_conf.xml. I used just the unchanged tool_conf.xml.main, which added more labels that now stay, and I emptied the tmp directory. Nothing helped. Any help is very much appreciated. Best regards, Sarah

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Error loading data
by SHAUN WEBB 24 May '12

24 May '12

Hi, I am reposting this message as I am still unsure what is causing this error. Also, when I go to the manage jobs page in the admin section I get the following message: This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs. I am running Galaxy as a single process on a standalone server, not sure what the problem is here. Would it help to send my universe_wsgi.ini file? Thanks Shaun ---- Hi, I have just upgrade my test version of Galaxy to the latest dist release and I am getting an error trying to load data either as an upload, a pasted entry or from UCSC. I have only altered conf files, any pointers to what could be causing this would be appreciated. The error is below: Traceback (most recent call last): File "/storage/home/galaxy/test/pre-dev/galaxy-dist/tools/data_source/upload.py", line 403, in <module> __main__() File "/storage/home/galaxy/test/pre-dev/galaxy-dist/tools/data_source/upload.py", line 378, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) AttributeError: 'Registry' object has no attribute 'load_datatypes' Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [galaxy-dev] Galaxy 'environment' variables
by Joachim Jacob 24 May '12

24 May '12

Dear Jean-François, But thanks for asking again, because now I had to look things up again, and now I found it. :-) Helping other people is apparently a strong drive to learn. The only variables I have found, are following variables below (See alsohttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?highlight=…) You can use them in the tool definition file as shown in example below. $GALAXY_HOME : /home/galaxy/galaxy-dist ${GALAXY_DATA_INDEX_DIR} :$GALAXY_HOME/tool-data $__new_file_path__ : universe_wsgi.ini's new_file_path --> temporary directory $__tool_data_path__ : tool_data_path value $__root_dir__ Top-level Galaxy source directory $__datatypes_config__ universe_wsgi.ini's datatypes_config value $__user_id__ Email's numeric ID $__user_email__ User's email address $__app__ (don't know about this one, seems to be deprecated) <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?highlight=%28m…> An example of what I like to do: I work with a 'configfile' to pass all parameters and galaxy settings to my tool/wrapper. *Tool definition file:* <tool ....> <command interpreter='perl'> my_program.pl $configfile </command> <inputs> ... configure here the inputs ... </inputs> <configfiles> <configfile name="$configfile"> param1==$param1 param2==$param2 ... ##Galaxy Environment Variables tempdir==${__new_file_path__}* *galaxyhome==${GALAXY_HOME} </configfile> </configfiles> <outputs> ... </outputs> <tests> </tests> </tool> *An my program 'my_program.pl' starts like:* #!/usr/bin/perl use strict; #------------ PARSE GALAXY ARGUMENTS # Get file with program parameters and Galaxy settings #---------------------------------------------------------------------------# my $configfile =$ARGV[0]; #------------- PARSE PARAMETERS # Parse parameters from config file #---------------------------------------------------------------------------## my (%para); open(CONFIG,"<$configfile"); while (<CONFIG>) { if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; } } close(CONFIG); exit 0; So now I have all parameters available in my program, in the hash %para, e.g. $para{'tempdir'}. Quick and easy! I hope this is clear, if not, just ask. Good luck with your implementation, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 05/23/2012 08:26 PM, Jean-Francois Payotte wrote: > Dear Joachim, > > I am interested at the exact same thing, such as finding a list of > 'environment' variables in Galaxy. > Did you ever got your answer? > > Best regards, > Jean-François > > > > *[galaxy-dev] Galaxy 'environment' variables* > > Joachim Jacob > Wed, 11 Apr 2012 08:18:46 -0700 > Hello all, > > Where can I find a list of 'environment' variables in Galaxy, such as: > $GALAXY_HOME > ${GALAXY_DATA_INDEX_DIR} > > > More specifically, I am looking for the temporary directory setting of > a user's Galaxy (as set in the universe_wsgi.ini). > > > Kind regards, > Joachim > > -- > Joachim Jacob, PhD > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > _http://www.bits.vib.be_ <http://www.bits.vib.be/> > @bitsatvib >

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Using workflows as components in workflows?
by Peter van Heusden 24 May '12

24 May '12

Hi there Is there a way in Galaxy to use workflows as components in workflows? I've got two datasets that start as Genbank files and are processed (features extracted, translated to AA) by a small workflow, and then BLASTed against one another. Ideally I'd like to modularise the initial steps as a workflow so that I can say input data goes through this workflow and then the result is fed into either the query or the subject slot of blastp. So is this possible? Thanks! Peter

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