galaxy-dev November 2011

galaxy-dev@lists.galaxyproject.org

83 participants
157 discussions

how is metadata generated
by KOH Jia Yu Jayce 27 May '12

27 May '12

Hi Just wondering how metadata files in galaxy-dist/database/files/_metadata_files are generated? Are there any configurations in the xmls that specify these to be generated? Thanks

7 17

debugging jobs in 'new' state
by Shantanu Pavgi 10 May '12

10 May '12

We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations: * No indication of new jobs in paster.log file * database/pbs script didn't contain any associated job scripts * in backend database - job table contained their galaxy job id but no command_line input was recorded Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful. -- Thanks, Shantanu.

3 4

Error on local galaxy using SAM-to-BAM tool on a cluster
by Carlos Borroto 12 Apr '12

12 Apr '12

Hi, I'm running into this error: "Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), " When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on "universe_wsgi.ini": # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at "sam_to_bam.py" I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran "samtools view ..." and "samtools sort ..." on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos

4 5

Defining Job Runners Dynamically
by John Chilton 05 Mar '12

05 Mar '12

Hello All, I just issued a pull request that augments Galaxy to allow defining job runners dynamically at runtime (https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-run…). Whether it makes the cut or not, I thought I would describe enhancements here in case anyone else would find it useful. There a couple use cases we hope this will help us address for our institution - one is dynamically switching queues based on user (we have a very nice shared memory resource that can only be used by researchers with NIH funding) and the other is inspecting input sizes to give more accurate max walltimes to pbs (a small number of cufflinks jobs for instance take over three days on our cluster but defining max walltimes in excess of that for all jobs could result in our queue sitting idle around our monthly downtimes). You might also imagine using this to dynamically switch queues entirely based on input sizes or parameters, or alter queue priorities based on the submitting user or input sizes/parameters. There are two steps to use this - you must add a line in universe.ini and define a function to compute the true job runner string in the new file lib/galaxy/jobs/rules.py. This first step is similar to what you would do to statically assign a tool to a particular job runner. If you would like to dynamically assign a job runner for cufflinks you would start by adding a line like one of the following to universe.ini cufflinks = dynamic:///python -or- cufflinks = dynamic:///python/compute_runner If you use the first form, a function called cufflinks must be defined in rules.py, adding the extra argument after python/ lets you specify a particular function by name (compute_runner in this example). This second option could let you assign job runners with the same function for multiple tools. The only other step is to define a python function in rules.py that produces a string corresponding to a valid job runner such as "local:///" or "pbs:///queue/-l walltime=48:00:00/". If the functions defined in this file take in arguments, these arguments should have names from the follow list: job_wrapper, user_email, app, job, tool, tool_id, job_id, user. The plumbing will map these arguments to the implied galaxy object. For instance, job_wrapper is the JobWrapper instance for the job that gets passed to the job runner, user_email is the user's email address or None, app is the main application configuration object used throughout the code base that can be used for instance to get values defined in universe.ini, job, tool, and user are model objects, and job_id and tool_id the relevant ids. If you are writing a function that routes a certain list of users to a particular queue or increases their priority, you will probably only need to take in one argument - user_email. However, if you are going to look at input file sizes you may want to take in an argument called job and use the following piece of code to find the input size for input named "input1" in the tool xml. inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) input1_file = inp_data[ "input1" ].file_name input1_size = os.path.getsize( input1_file ) This whole concept works for a couple of small tests on my local machine, but there are certain aspects of the job runner code that makes me feel there may be corner cases I am not seeing where this approach may not work - so your millage may vary. -John ------------------------------------------------ John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chilton(a)msi.umn.edu

3 2

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

2 1

Garli and Tandem Repeats Finder wrappers
by Oleksandr Moskalenko 08 Feb '12

08 Feb '12

I would like to avoid reinventing the wheel if possible, so I wonder if anyone has wrappers for Garli (https://www.nescent.org/wg_garli/Main_Page) and Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html) they could share. Thanks, Alex

2 2

Customizing the history panel
by Lukasse, Pieter 31 Jan '12

31 Jan '12

Hi, I'm looking for ways to customize the history panel that gets added to the workflow history after a step has finished. Below is the standard set of buttons/icons that we normally get: [cid:image001.png@01CCA9D3.2C2EF410] What I would like to do is to either add some extra buttons to it OR extend the functionality of such a button. How can this be done? I only found the page below mentioning there are some extra optional buttons, but it does not tell me how to enable/disable the buttons: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets Thanks and regards, Pieter Lukasse.

2 1

How to allow anonymous users to run workflows?
by Tim te Beek 29 Jan '12

29 Jan '12

Hi all, Was wondering how I can allow anonymous users to run workflows in my local Galaxy instance, as currently users need to be logged in to run workflows. I'd like drop this requirement in light of the intended publication of a workflow in a journal which demands that "Web services must not require mandatory registration by the user.". Could any you tell me how I can accomplish this? I've seen the option to use an external authentication method which could be employed to artificially 'login' anonymous users for a single session, but it appears this would also disable the normal users administration mechanisms in Galaxy, so I'm not sure this would be a good fit. Any hints on how to proceed, either via this route or otherwise, would be much appreciated. Best regards, Tim

2 3

MergeSamFiles.jar and TMPDIR
by Glen Beane 25 Jan '12

25 Jan '12

We recently updated to the latest galaxy-dist, and learned that the sam_merge.xml tool now uses picard MergeSamFiles.jar to merge the files instead of the samtools merge wrapper sam_merge.py. this is a problem for us because MergeSamFiles.jar does not honor $TMPDIR when creating temporary file names (the jvm developers inexplicably hard code the value of java.io.tmpdir to /tmp in Unix/Linux rather than doing the Right Thing) . On our cluster, TMPDIR is set to something like /scratch/batch_job_id/. This location has plenty of free space, however /tmp does not and now we can't successfully merge largeish bam files. In case anyone else is bit by this, I think there are two options the Picard tools take an optional TMP_DIR= argument that lets us specify the location we want to use for a temporary directory. Initially we ended up modifying the .xml to add TMP_DIR=\$TMPDIR to the arguments to MergeSamFiles.jar. This works, but we could potentially need to do this with multiple Picard tools and not just MergeSamFiles. Now I am probably going to go with the following solution: add something like "export _JAVA_OPTIONS=-Djava.io.tmpdir=$TMPDIR" to the .bashrc file for my Galaxy user. -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153

3 6

Galaxy installation with mysql database
by Alex R Bigelow 23 Jan '12

23 Jan '12

Hi, I am trying to install a local instance of Galaxy with an infobright mysql server; I created a database called "galaxy" (the user is also "galaxy," and it has all the privileges it should need), and the database_connection line is as follows: database_connection = mysql://galaxy:***********@localhost/galaxy?unix_socket=/tmp/mysql-ib.sock When I do this, I get the following error: Traceback (most recent call last): File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/gen21/alex/Apps/galaxy-dist/lib/galaxy/model/migrate/check.py", line 65, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 24, in __init__ self._load() File "/gen21/alex/Apps/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 36, in _load self.table = Table(tname, self.meta, autoload=True) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable sql = self._show_create_table(connection, table, charset) File "/gen21/alex/Apps/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table raise exc.NoSuchTableError(full_name) NoSuchTableError: migrate_version I found this question in the archives: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-March/002216.html As per both replies, I tried a virtual_env, which didn't work, and I also deleted the "galaxy" database so that it would create a fresh one, but, of course, now it can't connect to the database because it doesn't exist. How do I tell Galaxy to create the database it needs? Thanks again for all the support, Alex Bigelow

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galaxy-dev November 2011