May 2011 - galaxy-dev - lists.galaxyproject.org

downloading bam and bai files from sam-to-bam wrapper
by Ryan Golhar 01 Jun '11

01 Jun '11

In my local instance of Galaxy, I'm trying to download the BAM and BAI file from the tool SAM-to-BAM. I see the links for downloading the Dataset and bam_index. BTW - I'm running Safari on Mac OS X. When I download the Dataset, I get the BAM file. When I download the bam_index, it gets renamed to Galaxy13-[SAM-to-BAM_on...].bam_index.html The error is the extension, .bam_index.html. This should be .bam.bai. The BAM file gets saved correctly with .bam. I check the sam-to-bam XML wrapper but can't determine where this filename comes from or how to fix it. Has anyone else run into this? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

2 1

Multiple galaxy instances
by Jean-Baptiste Denis 01 Jun '11

01 Jun '11

Hello everybody, i'm in the process to provide Galaxy for multiple team. I've already setup a testing instance using the production setup page on the wiki (apache + sge) and it works quite well if i'm refearing to the users feedback. This setup is typically use for NGS dealing with data on a NFS share without uploading them to the instance. Why do i need multiple instance ? Maybe i'm not using galaxy correctly. Correct me if i'm wrong. My goal is to delagate the management of library/datasets to a galaxy admin of each team from the beginning : i do NOT want a SINGLE independant super admin to manage the access for multiple team, it doesn't scale. The galaxy instance and the underlying "galaxy" system user must access to the NGS data on the NFS (v3) share. This means that the galaxy user must be in a group that has access to the data. I can delegate the process of managing datasets and library to a dedicated galaxy admin. This setup is working quite well with the single instance setup. My job as a sysadmin is reduced to galaxy setup and maintenance : i'm not involved in the library/dataset management. The problem with this setup does not work if there is another team with data they don't want to share with others (don't blame me on that) : the galaxy system user must access the data of the first team AND the second team, this means that the galaxy admin of each team could access everything. One solution to this problem would be to have an independant galaxy super admin with access to everything which manage data access to each team. I don't like this solution, like i said, it doesn't scale. So, another way to deal with that is to give each team its own galaxy instance (each running with a specific system galaxy user) with a dedicated galaxy admin. Two possibility : - N galaxy tree, each with a different tuned universe_wsgi.ini init file (dedicated path, port, database, etc...). The problem here is on the sysadmin side : the update process effort must be repeated N times. - A unique galaxy tree, and N tuned (dedicated path, port, database, etc...) universe_wsgi.ini files. This seems the best to me but i need to know if galaxy internals can managed that kind of setup ? What do you think ? Any inputs, remarks or advices are welcome ! Regards, Jean-Baptiste

3 2

tmp directory not cleaned up?
by Ryan Golhar 01 Jun '11

01 Jun '11

I just noticed a lot of files in my galaxy tmp directory. Since this isn't a system tmp directory, the system cron scripts don't clean it up. Is there a galaxy cron script that can be used to clean up this directory? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

2 1

Error getting to http://galaxy/user/create on local instance
by Dave Walton 01 Jun '11

01 Jun '11

We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave

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MUMmer and TopHit filter
by Bossers, Alex 31 May '11

31 May '11

Our first tools arrived at the toolshed; The MUMmer genome comparison suite and a TopHit filter. Enjoy and we appreciate any feedback for improvement: http://community.g2.bx.psu.edu/tool/browse_tools?operation=tools_by_categor… Alex

1 0

stdout and stderr while using pbs
by shashi shekhar 31 May '11

31 May '11

Hi All, if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem. can i check the standard error before displaying anything on browser. Reagrds shashi shekhar

2 1

Accessing Data Library Template fields in tools?
by Duddy, John 31 May '11

31 May '11

I have my data in a data library and have a form template defined so I can enter the sample information. So, I import a data file into a history and want to run a tool on it. Can I pass the values of those form templates to my tool? Sort of line ${input.form_field_id} ? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

2 1

database table HistoryDatasetAssociation
by Harendra chawla 31 May '11

31 May '11

Hi, I am trying to modify the history_datset_association table in the database by adding one column, as per my requirement. I have changed the schema of the table but not able to add data for that column. Can anyone suggest how and where it can be done. Regards Harendra

2 1

Implemented adding tools via admin console
by Vossen, Bodo 31 May '11

31 May '11

Hi all, I've implemented functionality for adding tools via the admin menu. Let me just briefly explain what I did. You can upload a binary/script file to a specific folder (choosable). Then this file is analyzed. The analysis is at the moment only done for Perl/Python script, as those are mostly used in our institute. First, it is checked in what language the script is written in (if it is not a binary), then a syntax check is performed (for python pyflakes must be installed), and then it is checked how many arguments are in the script. Once you uploaded a file, you can add the XML file for this script. The XML file is analyzed as well, in the following matter. First it is checked that the XML is well formed. Then it is checked if the mandatory tags are in the XML ( I choosed for mandatory tags: root = tool, command, input, help ) Then it is checked if script and XML are "compatible" by checking if they have the same number of arguments. I also wrote unit tests for the main methods. They can be executed by "python lib/galaxy/util/test_tool_analysis.py" The main files I changed are lib/galaxy/web/base/controller.py lib/galaxy/util/tool_analysis.py lib/galaxy/util/helper.py lib/galaxy/util/tool_conf_helper.py and the templates for the admin in templates/admin The "update tools" is only done for one web process, there is no hup signal sent at the moment. If you have any questions or something is not working for you, please let me know, I probably have some time to check it. There are still some things that can be / should be implemented later on but I think this can be a good start for you guys. I forked galaxy-central, so you can check it out by cloning https://bitbucket.org/Bodolski/galaxy-central-adding-tools hg clone https://Bodolski@bitbucket.org/Bodolski/galaxy-central-adding-tools If you have any comments or question please do not hesitate to contact me, I'm open for every kind of critics. Best wishes from Germany, Bodo Vossen

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Import Library Datasets into Histories - automatically imports into current AND new history - Bug?
by Liisa Koski 31 May '11

31 May '11

Hello, I noticed a change in the newest version. When importing Library Datasets into Histories...if you enter a New History name for the destination Galaxy will import into the new AND current history. So it is getting imported into two histories. Is this a bug? It would really be nice to only import a dataset into a new history like before. Thanks, Liisa

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