May 2012 - galaxy-dev - lists.galaxyproject.org

Value error when running run.sh
by julie dubois 16 May '12

16 May '12

Hi, I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL I've configured apache 2 with this lines on file /etc/apache2/sites-available/default between <VirtualHost> and </VirtualHost> : <Proxy "http://localhost:8080"> Order Deny,Allow Allow from all </Proxy> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/chevalier/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/chevalier/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/chevalier/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/chevalier/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/chevalier/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy/(.*) http://localhost:8080$1 [P] I've configured my MYSQL with a user who have all privilegies on a database and in the universe_wsgi.ini the connection database appears like this : database_connection = mysql://cistrome:cistrome@localhost :/var/run/mysqld/mysqld.sock/cistromeap After running sh run.sh in my galaxy directory, I obtain this error message : .... File "/home/chevalier/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 49, in __init__ self.port = int(port) ValueError: invalid literal for int() with base 10: ' ' This is the case too when I run this with root privilegies. Is it an error in my configuration of apache 2 or in MySQL ? Or is it an error in my universe_wgsi.ini ? Thank you Julie

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Follow Up
by Daniel Patrick Sullivan 16 May '12

16 May '12

Hi, Galaxy Developers, I sent an email to this list earlier this week regarding an issue I was having with the 'schedule jobs as user' functionality of Galaxy. I am taking a closer look at the documentation on this configuration option, and based on my reading, this feature is only supported with DRMAA (and not PBS). Based on my reading of the cluster URL in the galaxy documentation (http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster) it is my understanding that galaxy must use PBS to interact with TORQUE; the documentation specifically states "although for legacy reasons, pbs_python is used for TORQUE". Does this mean that I am not able to use the schedule jobs as user functionality of galaxy with TORQUE? Is DRMAA not supported with TORQUE at all for Galaxy? Dan Sullivan

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Re: [galaxy-dev] ? IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
by Josh Nielsen 16 May '12

16 May '12

I have seen this error many times (for various mako.py files) and it is often either when the user running it has insufficient privileges or the file permissions on a folder (could be several directories upstream) or a file have changed in some way. If you do a 'ps -ef | grep python' do you see the paster.py process running with your expected user? Do you use sudo to elevate the privileges when you run it? I use a 'galaxy' user but I execute run.sh (which I have created a service script for in /etc/init.d) with sudo while logged in as galaxy. Also you might want to do an 'ls -l' in the compiled_templates/ directory and look at the file permissions and file ownership. -Josh

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Re: [galaxy-dev] user data upload directory structure
by Josh Nielsen 16 May '12

16 May '12

Ah, yes. This is what I was just requesting yesterday in the email that I sent, although it was much more long-winded. I didn't see this email chain from the day before. Having a user-representative directory structure would be beneficial in my mind. I followed/understood your suggested directory structure up until the arrows. Are those supposed to be symlinks? If so, what do you have in mind? I was thinking that just having those subdirectories by user id under files/ would be enough (although I could see how you could symlink them to some other arbitrary location if you so desired). My desired application was so that I could set up an FTP share to the files/ directory so that our users could copy their (processed) files off of the Galaxy server to other servers in our environment as well as one of our other clusters. Having the datasets segregated into the user's/owner's subdirectories would make it easier to identify and copy them off for that purpose. -Josh >Nate- >I do know about the disk accounting/quota features of Galaxy >As I eluded in my previous email, it goes beyond accounting actually. I >wanted to be able to implement something like: >~/galaxy-dist/database/files/user_id_000 -> /one_data_pool_set/id_000 >~/galaxy-dist/database/files/user_id_001 -> /another_data_pool_set/id_001 >which would match the usual data placement from a scheduler perspective too. >I'll look at galaxy-dist/lib/galaxy/objectstore/__init__.py >Thanks a lot >JC

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Newbie question, adding a custom perl script
by Mac 16 May '12

16 May '12

Hi, A co-worker has a perl script that takes a directory path, and then interates over a the file in that directory and processes them into an output directory. I want to integrate that into galaxy. I've figured out that I'll need to create a tool XML conf with the inputs , outputs etc. My question is what param type should I use for a directory, in the input and output ? Or maybe what I'm looking for a is an input, output type that is a set of file (rather than tying it to a filesystem) Sorry for my beginners questions ! Thanks Mac

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Re: [galaxy-dev] Internal Server Error when using Galaxy API
by liram_vardi＠agilent.com 16 May '12

16 May '12

Hi, I found the solution. I had to update the Tophat wrapper XML from Galaxy repository, in order to be computable with the newer version of Tophat that we have. Hope this post will be informative to someone. Thanks, Liram From: VARDI,LIRAM (A-Labs,ex1) Sent: Tuesday, May 15, 2012 5:57 PM To: Galaxy Dev (galaxy-dev(a)bx.psu.edu) Cc: BEN-DOR,AMIR (A-Labs,ex1); TSALENKO,ANYA (A-Labs,ex1) Subject: Internal Server Error when using Galaxy API Hi all, I have a strange problem when I am trying to run workflow using Galaxy API. If the workflow contains Tophat for Illumina, then when I am trying to use the "submit" API script in order to execute this workflow on some input dataset, I am strangely getting this HTTP error: "Error. 500 Internal Server Error The server has either erred or is incapable of performing the requested operation." Although the server has returned an error message, when I checked the "saved histories" I could notice that the job was successfully submitted and it is running! When I removed TopHat from the workflow, no error was returned... The thing is that I need the "dictionary" that is returned by the "submit" script. Has anyone encountered this problem before and know how to solve it? Thanks in advance! Liram

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Accessing different folder's datasets
by Ciara Ledero 16 May '12

16 May '12

Hi all, I have just created scripts that ran velveth, velvetg and oases. The outputs of these commands are kept in a separate folder. Is it possible to show the data stored in this folder in our Galaxy web page? Or I don't have a choice but to upload them? Cheers, CL

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user data upload directory structure
by Jean-Christophe Ducom 15 May '12

15 May '12

All- Is there a way to change the upload default directory structure (/database/files) to organize files per user_id instead? something along the following lines ~galaxy-dist/database/files/postgresql_user_id0 ~galaxy-dist/database/files/postgresql_user_id1 Thank you JC

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Internal Server Error when using Galaxy API
by liram_vardi＠agilent.com 15 May '12

15 May '12

Hi all, I have a strange problem when I am trying to run workflow using Galaxy API. If the workflow contains Tophat for Illumina, then when I am trying to use the "submit" API script in order to execute this workflow on some input dataset, I am strangely getting this HTTP error: "Error. 500 Internal Server Error The server has either erred or is incapable of performing the requested operation." Although the server has returned an error message, when I checked the "saved histories" I could notice that the job was successfully submitted and it is running! When I removed TopHat from the workflow, no error was returned... The thing is that I need the "dictionary" that is returned by the "submit" script. Has anyone encountered this problem before and know how to solve it? Thanks in advance! Liram

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parameters going into quality scores fastq Illumina
by Claudia Gottstein 15 May '12

15 May '12

Hi, I would like to understand which parameters, ideally which algorithm go into the scores one obtains from the quality statistics out of fastQ illumina data. What is this score composed of? And how come that applying fastq groomer and then using fastq summary statistics tool gives a different score as using the fast q qc from babraham. I heard fastq groomer may change the data? EXAMPLE: In my example the scores using fastq groomer and then fastq summary statistics were between 3 and 11, whereas using fastq qc straight on the data the score was between 32 and 41. Thank you so much for your explanation. Best regards, CG

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