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

error on fastq file while grooming or fastqc report or fastqc converter
by Wetzels, Yves [JRDBE Extern] 17 Feb '12

17 Feb '12

Dear I am receiving the same error over and over again "WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'coverage', using datatype from /mnt/galaxyData/tmp/tmpuTitVp." Whether I run - Fastqc: Fastqc QC <http://ec2-107-21-142-14.compute-1.amazonaws.com/tool_runner?tool_id=fa stqc> using FastQC from Babraham - FASTQ Groomer <http://ec2-107-21-142-14.compute-1.amazonaws.com/tool_runner?tool_id=fa stq_groomer> convert between various FASTQ quality formats Anybode any idea ? Kind Regards Yves

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Re: [galaxy-dev] LDAP authentification
by Sarah Maman 17 Feb '12

17 Feb '12

Hello, I managed to connect to Galaxy to LDAP ;-) Three points were blocking for me: * Being root of my virtual machine can carry out tests * I confused login / password of two LDAP, so I thought that my authentication method was not good while I was using the wrong password ... * It is better not to go through a proxy 1 - Set configuration file of Galaxy: universe_wsgi.ini to delegate user authentication to an upstream proxy Apache: Users and Security use_remote_user = True remote_user_maildomain = toulouse.inra.fr 2 - Create a file type "htaccess" file named galaxy.conf (in / etc / httpd / conf.d /): For reasons of performance and safety, it is advisable not to use a. htaccess but a galaxy.conf file in the main server configuration (Apache), because the latter will be charged a once when the server starts. With an .htaccess file, this file will be charged at each access. RewriteEngine on <Location "/galaxy"> # Define the authentication method AuthType Basic AuthName "Galaxy" AuthBasicProvider ldap AuthLDAPURL "ldap :/ / server URL: 389/..." AuthzLDAPAuthoritative off Require valid-user RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e </ Location> RewriteRule ^ / $ galaxy / galaxy / [R] RewriteRule ^ / galaxy / static / style / (. *) / var/www/html/galaxy/static/june_2007_style/blue / $ 1 [L] RewriteRule ^ / galaxy / static / scripts / (. *) /vVar / www / html / galaxy / static / scripts / packed / $ 1 [L] RewriteRule ^ / galaxy / static / (. *) / var / www / html / galaxy / static / $ 1 [L] RewriteRule ^ / galaxy / favicon.ico / var / www / html / galaxy / static / favicon.ico [L] RewriteRule ^ / galaxy / robots.txt / var / www / html / galaxy / static / robots.txt [L] RewriteRule ^ / galaxy (. *) http://ip:port $ 1 [P] As Galaxy is not installed in root directory but in a galaxy directory (var / www / html / galaxy /), so following changes are needed: 1 - Add a RewriteRule 2 - Do not go through a proxy 3 - REMOTE_USER variable is AUTHENTICATE_uid ( AUTHENTICATE_ sAMAccountName for Windows AD) 4 - To generate dynamic URLs, it is necessary to configure prefix in universe_wsgi.ini : [Filter: proxy-prefix] use = egg: # prefix PasteDeploy prefix = / galaxy [App: main] filter-with = proxy-prefix cookie_path = / galaxy If you are not root on the virtual machine, create a symlink from / etc / httpd / conf.d / to galaxy.conf 3 - Some useful checks Verify Apache version and Apache modules because each directive must have an associated module: Directive → Related module (which mod_ldap) AuthType → mod_auth_basic.so AuthBasicProvider → mod_authnz_ldap and mod_authz_ldap Rewrite (for proxy) → mod_rewrite.so RequestHeader→ mod_headers Check that the galaxy is installed on ldap using this command: ldapsearch-x-h LDAP URL : port-b "dc" When you make a modification in galaxy.conf, restart Apache (or graful). In httpd.conf, so that access management is authorized by the file. # # AccessFileName: The name of the file to look for in EACH directory # For additional configuration directives. See also the AllowOverride # Directive. # AccessFileName. Htaccess Check: Chmod 777 galaxy.conf 4 - Finally, restart run.sh (sh run.sh &) Thanks A LOT for your help, Sarah

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Expanding galaxyTool volume?
by Dave Lin 16 Feb '12

16 Feb '12

Hi All, What is the recommend process for expanding the galaxyTool volume for an existing galaxy instance (using EC2/cloudman)? I tried the following, but it didnt' work for me. 0) Terminate cluster. 1) Amazon EC2- create snapshot of current galaxyTools volume 2) Amazon EC2- create volume from step 1 + specify desired volume size. 3) Amazon EC2- create new snapshot from Step 2. 4) Amazon S3- identify S3 bucket for this cluster. Modify persistent_data.yaml. Modify size and snap_id to correspond with step #3 5) Amazon EC2- Start new instance-- using same AmazonID + ClusterName I was expecting the new instance to startup and create a galaxyTools volume based on the snapshot identified in the persistent_data.yaml file, but that didn't seem work. Thanks in advance for any pointers. Dave

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Tool that outputs html report
by Daniel Sobral 16 Feb '12

16 Feb '12

Hello, I want to develop a galaxy wrapper for a tool that outputs an html report (with images inside specific subfolders). Do I need to do like the FastQC galaxy wrapper that reconstructs the html so that they are all in the same folder? Or is there a way to circumvent this so that I can keep the original html structure? One way of "cheating" is maybe zipping the output and provide the zip file as data? Thanks, Daniel Sobral

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which galaxy version is on the AMI?
by Jorrit Boekel 15 Feb '12

15 Feb '12

Dear list, As a first attempt to put my tools in the cloudman/galaxy environment, I have tried to just crudely copy them to their respective directories, along with tool_conf.xml. This worked, but some tools raise errors upon loading them that I cannot reproduce in my local Galaxy instance (neither in a galaxy-dist, nor in a galaxy-central fork). Something with required "value" fields in some <param> tags (some of which are optional="true"). I would thus like to know which Galaxy fork/branch/version is running on the most recent AMI (March 2011 I believe), to be able to troubleshoot this locally. In case it would be a somewhat older Galaxy that is in the AMI, is there a way to update it (via hg), or a manual that shows how to check out a full cloudman/galaxy/SGE environment on an otherwise empty ubuntu-EC2 instance? cheers, jorrit

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Re: [galaxy-dev] [galaxy-user] While executing tool galaxy giving this error
by Dannon Baker 15 Feb '12

15 Feb '12

Hi, This is not a tool from our distribution. Please send questions about local instances, core galaxy development, or your own tool development to the galaxy-dev(a)lists.bx.psu.edu mailing list and *not* this galaxy-user mailing list. That said, if you could provide more information about what's going on here (structure of getsitesnotoverlap_tf, etc) I might be able to give a few pointers. Thanks! -Dannon On Feb 15, 2012, at 3:28 AM, La Chi wrote: > hi, > will you please help me how can i fix this error' > thanks > > > Traceback (most recent call last): > File "/galaxy-dist/tools/ova/getsitesnotoverlap_tf.py", line 60, in ? > if __name__ == "__main__": __main__() > File "/galaxy-dist/tools/ova/getsitesnotoverlap_tf.py", line 50, in __main__ > result_set = connection.execute( "select * from getsitesnotoverlap_tf (" + userid + "," + tfid + "," + bpover + "," + ch + "," + sf +")" ) > File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 824, in execute > return Connection.executors[c](self, object, multiparams, params) > File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 888, in _execute_text > return self.__execute_context(context) > File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 896, in __execute_context > self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) > File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute > self._handle_dbapi_exception(e, statement, parameters, cursor, context) > File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception > raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) > sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "chr1" does not exist > LINE 1: select * from getsitesnotoverlap_tf (6,149,-1000,chr1,tf) > ^ > 'select * from getsitesnotoverlap_tf (6,149,-1000,chr1,tf)' {} > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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bug: unsorted bam files and import into data library
by Florian Wagner 15 Feb '12

15 Feb '12

Hi, when a tool outputs an unsorted bam file, the indexing fails (quietly) and its metadata variable "bam_index" points to an inexistent file. This causes a nasty bug when trying to import the dataset into a data library and actually makes the library unusable unless you delete the broken entry from the - in my case Postgresql - database by hand. Are you working on it? Thanks, Florian

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Re: [galaxy-dev] No Display at UCSC Main link.
by Jennifer Jackson 14 Feb '12

14 Feb '12

Hello again, The link is not a Galaxy Main public instance share link, which would start with: http://main.g2.bx.psu.edu Having the datatype as BED and the database as hg19 would (for all of the cases I can think of) bring up the "View at UCSC" link, if the instance is set up to have "display at UCSC" configured. So, the root cause of the problem is probably with how this other instance is set up. If this is not your instance, you will want to contact the folks running it to see if they have plans to configure UCSC display. If this is yours, follow the instructions on this wiki to get set up: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy See the section: Display at UCSC Hopefully this helps, Best, Jen Galaxy team On 2/14/12 9:26 PM, Luobin Yang wrote: > Hi, Jen, > > The dataset is BED datatype and the database is hg19. Actually this > history contains the same steps as those in Galaxy101 tutorial. > > I created the link for the history and here it is: XXXXXXXXXXXXXXXXXXXXXXXXXXXX > > So basically I do not see an option called "Display at UCSC Main", but > it has two other options, "View in GeneTrack" and "Display at Ensemble > Current" > > Thanks, > Luobin > > On Tue, Feb 14, 2012 at 9:35 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Luobin, > > To display at UCSC, the datatype has to be a UCSC display type and > the database has to be a UCSC genome browser. Often, small changes > can be made to tune a dataset to help it fit into these > requirements. Other times, a dataset will need to be transformed > into another type or it can't be viewed at all because the genome is > not available at UCSC. > > You should try to modify these attributes yourself first. Common > UCSC datatypes from Galaxy are: BED, bigBED, BAM. For the list of > UCSC known datatypes, see: > http://genome.ucsc.edu/FAQ/__FAQformat.html > <http://genome.ucsc.edu/FAQ/FAQformat.html>. > > Known databases would be any that you also can find at: > http://genome.ucsc.edu as full genome assemblies. The short label > used at UCSC should match the database assignment at Galaxy. For > example, the most recent human would be "hg19" at both. > > If you are still stuck and would like to send me a shared history > link, I can provide feedback about how to modify (if possible) to > view at UCSC. Use "Options -> Share or Publish", generate the link, > and email this link directly back to me. Be sure to include the > dataset #, so that I know which in your history you want to view at > UCSC. > > Best, > > Jen > Galaxy team > > > On 2/14/12 11:50 AM, Luobin Yang wrote: > > Hi, > > I have a local instance of Galaxy, but I found there is no > "Display at > UCSC Main" link for some datasets that can be viewed in GeneTrack or > displayed by Ensemble, what has been wrong? > > Thanks, > Luobin > > > _____________________________________________________________ > 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/ > > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/__Support > <http://galaxyproject.org/wiki/Support> > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Support for PolyPhen2
by Praveen Raj Somarajan 14 Feb '12

14 Feb '12

Hi Dev Team, Do you have any plan to integrate PolyPhen2 to Galaxy? I feel, it would be good if you can, as this extends the functionality of NGS analysis and (definetly) it would be value addition to Galaxy as well. Let me know your comments. Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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No Display at UCSC Main link.
by Luobin Yang 14 Feb '12

14 Feb '12

Hi, I have a local instance of Galaxy, but I found there is no "Display at UCSC Main" link for some datasets that can be viewed in GeneTrack or displayed by Ensemble, what has been wrong? Thanks, Luobin

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