galaxy-dev July 2013

galaxy-dev@lists.galaxyproject.org

133 participants
209 discussions

Adding GATK tools to Galaxy Cloudman
by Iry Witham 12 Aug '13

12 Aug '13

Hi Team, I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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cummerBund installation
by sridhar srinivasan 12 Aug '13

12 Aug '13

Dear Developers, Could you please tell me the possibilities of using the R package cummeRband for visualization of RNA-seq data in galaxy?? Thanks Sridhar

3 2

support pbkdf2 in proftpd 1.3.5rc3
by Leon Mei 09 Aug '13

09 Aug '13

Dear galaxy developers, We have tried today to upgrade our proftpd configuration to make uploading for our galaxy users possible again, both for users with "old" as well as "new" style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3 and have the following SQL part in our configuration file based on the post of http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295… SQLEngine on SQLLogFile /var/log/proftpd-sql.log SQLBackend postgres SQLConnectInfo galaxy@localhost:5840 galaxyftp <[ourpassword]> SQLAuthTypes SHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1000 24 SQLPasswordUserSalt sql:/GetUserSalt SQLAuthenticate users SQLDefaultUID 108 SQLDefaultGID 116 SQLDefaultHomedir /opt/cloudman/pkg/proftpd/var SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE password END) AS password2,'108','116','/mnt/galaxyData/tmp/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U'" We have executed the LookupGalaxyUser and GetUserSalt commands manually, and the results look good. Now, old users can login via ftp, but for a new user, the authentication still fails: 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: >>> cmd_check 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'sha1' 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: 'sha1' SQLAuthType handler reports failure 2013-07-26 13:15:06,989 mod_sql/4.3[31761]: checking password using SQLAuthType 'pbkdf2' 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler reports failure What are we missing? Thanks! Rob and Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl<https://wiki.nbic.nl/index.php/Next_Generation_Sequencing> Skype: leon_mei Mobile: +31 6 41709231

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ActionInputError undefined
by Jim Johnson 08 Aug '13

08 Aug '13

I was using the quotas api to update a quota amount and got the error: galaxy.web.framework ERROR 2013-07-30 15:40:59,149 Uncaught exception in exposed API method: Traceback (most recent call last): File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 189, in decorator rval = func( self, trans, *args, **kwargs) File "/Users/jj/gxt/gxt/lib/galaxy/web/framework/__init__.py", line 221, in decorator return func( self, trans, *args, **kwargs ) File "/Users/jj/gxt/gxt/lib/galaxy/webapps/galaxy/api/quotas.py", line 108, in update except ActionInputError, e: NameError: global name 'ActionInputError' is not defined Was ActionInputError meant to be a class in lib/galaxy/exceptions/__init__.py ? diff -r 951e853b0bcd lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py Tue Jul 30 12:54:02 2013 -0400 +++ b/lib/galaxy/exceptions/__init__.py Tue Jul 30 16:38:50 2013 -0500 @@ -21,6 +21,9 @@ class ItemOwnershipException( MessageException ): pass +class ActionInputError( MessageException ): + pass + class ObjectNotFound( Exception ): """ Accessed object was not found """ pass -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

2 1

Appending _task_%d suffix to multi files
by Alex.Khassapov＠csiro.au 07 Aug '13

07 Aug '13

Hi guys, We've been using Galaxy for a year now, we created our own Galaxy fork where we were making changes to adapt Galaxy to our requirements. As we need "multiple file dataset" - we were using Johns' fork for that initially. Now we are trying to use "The most updated version of the multiple file dataset stuff" https://bitbucket.org/msiappdev/galaxy-extras/ directly as we don't want to maintain our own version. One of the problems we have - when we upload multiple files - their file names are changed (_task_%d suffix is added to their names). On our branch we simply removed the code which does it, but now we wonder if it is possible to avoid this renaming somehow? I.e. make it configurable? Is it really necessary to change the file names? -Alex -----Original Message----- From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Jorrit Boekel Sent: Thursday, 25 October 2012 8:35 PM To: Peter Cock Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] the multi job splitter I keep the files matched by keeping a _task_%d suffix to their names. So each task is matched with its correct counterpart with the same number. cheers, jorrit

4 6

Invalid Galaxy URL: None - Installing Tools Shed
by Adam Brenner 06 Aug '13

06 Aug '13

Howdy, I am trying to install a tools shed item, Emboss, but when I do this via the admin interface, I get the following text: Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable cookies in your browser. I have searched the universe_wsgi.ini file and could not find anything that looks like Galaxy URL. Any ideas on how to set the Galaxy URL? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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lessc compiler error on blue_colors.ini
by Seth Sims 05 Aug '13

05 Aug '13

Dear Galaxy devs, I am attempting to create a style directory to match my school's look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error: ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FFFFFF I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process. - Seth

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Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
by Peter Cock 02 Aug '13

02 Aug '13

On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Björn, > > This one has been applied in changeset 10219:a7edac403b6c, and all of > your patches are now running on the test tool shed. > > Thanks very much, > > Greg Von Kuster Hi Greg & Björn, I think supporting reStructuredText is a good idea, but should not be done automatically, consider: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 This README file is named with the extension *.txt and does not render nicely if treated as *.rst, things like "System Message: ERROR" and "System Message: WARNING" are shown to the user. I suggest that the ToolShed only render like this if the README file is using the *.rst extension, but otherwise default to plain text (e.g. no extension or *.txt files). Thanks, Peter

2 3

Choosing which nodes to run on for a whole history (Galaxy cluster)
by Ben Gift 02 Aug '13

02 Aug '13

I'm setting up Galaxy and Torque with my cluster and I was wondering if I could set it up so that nodes could be assigned for a whole history. This way I can re-run histories on certain nodes for benchmarking runtimes. It seems that the closest I can get with the built in functionality is specifying nodes on a per-tool basis, which is good but it would be painful to have to specify this for each tool I use in a pipeline each time. So how difficult would it be for me to add this feature, and which files should I start with in the code base? Or have I misunderstood and this is actually built in? Thanks

2 1

Next Galaxy Release date (and Tool Shed update)?
by Peter Cock 01 Aug '13

01 Aug '13

Hi all, Is there a target date for the next Galaxy release, or should that differ, the next update to the main Tool Shed? I'd like to start using reStructuredText README.rst files in my tools which render much more nicely on the Test Tool Shed, but are currently ignored on the Main Tool Shed (since it doesn't yet have the updates to look for and display *.rst files). Thanks, Peter

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galaxy-dev July 2013