February 2013 - galaxy-dev - lists.galaxyproject.org

Problem referencing EMBOSS tools in universe_wsgi.ini
by Guest, Simon 06 Feb '13

06 Feb '13

We have set up our local Galaxy installation to submit jobs by default through HTCondor, using the drmaa tool runner. We override this on a tool-by-tool basis in universe_wsgi.ini, to specify certain tools we always want to run locally. The problem is that EMBOSS tools have a tool id like 'emboss: infoseq46', and it's not possible to reference a tool with an id containing a colon in the universe_wsgi.ini file (because colon is the character which separates a configuration item name from its value). It seems to me there are two possible solutions: 1. Implement some form of escape character processing in the config file parser (on top of Python's ConfigParser) so we can write tool ids in that file like 'emboss%3a infoseq46' 2. Change all the EMBOSS tools to have ids like 'emboss-infoseq46' rather than using a colon and space. For now, we are modifying our XML files locally (with a script) to do 2. Are there any comments from Galaxy developers on which of these solutions they prefer, or any reason why (2) shouldn't be incorporated in the Galaxy mainline? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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Bcftools to convert bcf to vcf
by sunearth Wu 06 Feb '13

06 Feb '13

I run my own files against my own reference with bowtie. In order to obtain SNPs, I use Mpile to get .bcf file. When I try to use bcftools to convert bcf to vcf. The output is always "tabuler" and size of file always less than 1k. It seems like the system can't process my bcf. Is there any setting I should apply or any setting I should modify? In previous steps, I didn't change any setting. Thank you

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Manager assigns job but it never reaches the handler
by Nikoloas Sidiropoulos 06 Feb '13

06 Feb '13

Hi all! When user tried to run Phantom Peak, the job was assigned to a handler by the manager but it keeps hanging. No messages appear on the handler.log file. As an admin I can use the tool successfully with no abnormal behavior. When the user deleted the job, the following message appeared on the handler.log galaxy.jobs.handler DEBUG 2013-02-06 17:51:49,591 Stopping job 296: galaxy.jobs.handler DEBUG 2013-02-06 17:51:49,592 stopping job 296 in local runner galaxy.jobs.runners.local WARNING 2013-02-06 17:51:49,613 stop_job(): 296: no PID in database for job, unable to stop /steno-internal/projects/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * Do you have any idea why this would happen? Regards, Nikos

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JAVASCRIPT error - ctd.
by Joachim Jacob |VIB| 06 Feb '13

06 Feb '13

Hi all, Occasionally, a JAVASCRIPT error appears. I think now this has to do with the app running Galaxy embedded (Fogger). This time, when I run a workflow on multiple input files (fastqc on a bunch of fastq files). The Javascript error is: ERROR updating hdas from api history contents:efd5a801e04dff8d,aa41b6bf76b5d046,399f7558b6aa905b,2817a997b5242e3d,58a41d419e31105a,2377f6835e89edaf,1fb058b7916cd73f The relating entry in the web log is: web12.log:193.191.128.2 - - [06/Feb/2013:11:37:19 +0200] "GET /api/histories/10fc65318d20c004/contents?ids=efd5a801e04dff8d%2Caa41b6bf76b5d046%2C399f7558b6aa905b%2C2817a997b5242e3d%2C58a41d419e31105a%2C2377f6835e89edaf%2C1fb058b7916cd73f HTTP/1.1" 200 - "http://galaxy.bits.vib.be/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+" Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Re: [galaxy-dev] Velvet program files
by Thyssen, Gregory - ARS 06 Feb '13

06 Feb '13

I also figured this one out, My external USB harddrive name had a space in it. So velvet is running for the first time... Got my fingers crossed. Thanks for all the help; I'm sure Ill need some later. Greg From: Thyssen, Gregory - ARS Sent: Tuesday, February 05, 2013 3:34 PM To: 'galaxy-dev(a)bx.psu.edu' Subject: RE: Velvet program files I partially answered my own questions by reading the Tool Dependencies wiki page. I installed velvet to my workstation. When I open the shell to start galaxy, I modify $PATH to include the velvet directory. Now the error I get in Velvet suggests it found the program, but something else is wrong. My new error is: No reads found The reads are fastq files that appear in my history and are data libraries housed in an external harddrive. I have used these same data before on the public server. Please advise, Thanks, Greg From: Thyssen, Gregory - ARS Sent: Tuesday, February 05, 2013 10:38 AM To: 'galaxy-dev(a)bx.psu.edu' Subject: Velvet program files So I am setting up my local Galaxy on a workstation for my own use. I have installed several programs from the Assembly Main Tool Shed. None works. Are these just the wrappers? Do I need to install, say, Velvet somewhere outside of Galaxy? How do I do this? My errors: 6: velveth on data 2 error An error occurred running this job:Unable to run velveth: No such file or directory 7: Abyss on data 5 error An error occurred running this job: ERROR: Expected exactly 3 arguments; got: 67 /media/My Passport/IM-Data2Bio-10262012/IM-mut1/Im-mutant-bulk_1.fastq /home/galaxy/galaxy-dist/database/files/000/dataset_9.dat 8: MIRA contigs (FASTA) error An error occurred running this job: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/3e7eca1f5d04/mira_assembler/tools/sr_assembly/mira.py", line 33, in mira_ver = get_version() File "/home/galaxy/shed_tool 15: Singleton reads reads for velvet error An error occurred running this job: Error running preppereads.sh /bin/sh: /users/galaxy/galaxyscripts/prepare_pe_reads_for_velvet.sh: No such file or directory Thanks, Greg This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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Can Galaxy run on Hadoop system?
by lukeyoyo 06 Feb '13

06 Feb '13

Hi, I am a computer engineer and have to deploy a cloud computing system, like Hadoop. I want to deploy a local Galaxy system on the Hadoop platform. I know that Galaxy can run on Cloud such as EC2 from Amazon. My question is: can Galaxy run on Hadoop? (Not running within a virtual mechine, but interacting with multiple slave nodes in Hadoop) If NOT, do you have any plan to migrate it to Hadoop platform? Best regards. lukeyoyo

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Re: [galaxy-dev] Why
by Dannon Baker 06 Feb '13

06 Feb '13

Have you restarted your galaxy instance after changing the setting? And, in that drop-down, can you confirm that 'filesystem paths' is not an option? Also, please keep conversations on-list so that others might be able to help and/or benefit from the exchange. -Dannon On Feb 5, 2013, at 12:15 PM, hudaiber(a)icgeb.org wrote: > I set allow_library_path_paste = True in universe_wsgi.ini and still don't have the option of copying locally on manage data libraries page. > > http://i.imgur.com/PEeCAnc.png?1 > > Should I set some other parameters to True? > > <quote author='Dannon Baker'> > The absolute fastest method would be to enable filepath upload for data > libraries (in universe_wsgi.ini -- allow_library_path_paste = True). Once > that's set, you can paste the absolute file path into the upload box, and > check the box for not copying the data. This will leave the data where it > is on the external drive, though it will make it available in the Data > Library. Obviously if you use this method, you'll need to have that > external drive attached (and always at the same mount point) to use the > data. > > If you actually *do* want to copy this data off the external drive, simply > don't check that 'no copy' checkbox and the data will be copied directly > through the filesystem and not uploaded. > > -Dannon

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Empty status for web uploaded non-empty datasets
by Eric Enns 06 Feb '13

06 Feb '13

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One-to-many relationship assocation
by Ted Goldstein 05 Feb '13

05 Feb '13

I am trying to define a colleagues association table that can be used to notify people when there colleagues make changes. Think of it as a Facebook "followers" type of thing. The relationship is not necessary inverse. I may follow James Watson, he might not (yet) follow me. ;-) Anyhow, here is where I am at, but SQL Alchemy wants a fully bidirectional relationship and complains Colleague_Association.table = Table( "colleague_association", metadata, Column( "id", Integer, primary_key=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "colleague_user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) , Column( "deleted", Boolean, default=False ) ) assign_mapper( context, Colleague_Association, Colleague_Association.table, properties=dict( user=relation( User, backref="colleagues" ), colleague=relation( User ) )) There are examples on the web for doing this in more recent versions of SQLAlchemy, but I can't find one that uses the (now deprecated) assign_mapper method. Any ideas? Thanks, Ted

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Velvet program files
by Thyssen, Gregory - ARS 05 Feb '13

05 Feb '13

So I am setting up my local Galaxy on a workstation for my own use. I have installed several programs from the Assembly Main Tool Shed. None works. Are these just the wrappers? Do I need to install, say, Velvet somewhere outside of Galaxy? How do I do this? My errors: 6: velveth on data 2 error An error occurred running this job:Unable to run velveth: No such file or directory 7: Abyss on data 5 error An error occurred running this job: ERROR: Expected exactly 3 arguments; got: 67 /media/My Passport/IM-Data2Bio-10262012/IM-mut1/Im-mutant-bulk_1.fastq /home/galaxy/galaxy-dist/database/files/000/dataset_9.dat 8: MIRA contigs (FASTA) error An error occurred running this job: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/3e7eca1f5d04/mira_assembler/tools/sr_assembly/mira.py", line 33, in mira_ver = get_version() File "/home/galaxy/shed_tool 15: Singleton reads reads for velvet error An error occurred running this job: Error running preppereads.sh /bin/sh: /users/galaxy/galaxyscripts/prepare_pe_reads_for_velvet.sh: No such file or directory Thanks, Greg This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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