- galaxy-dev - lists.galaxyproject.org

missing "fastq groomer" tool on galaxy cloudman
by NAMIT KUMAR 13 Oct '14

13 Oct '14

Hello, I am using galaxy on amazon web servers ( AMI: ami-a7dbf6ce; Name: Galaxy CloudMan 2.3). This is a setup I have used several time in the past with no issue, for suddenly since yesterday- there is *NO option of fastq groomer tool* on this ami. fastq groomer tool is still available on public server but not on aws cloudman. Anyone has any information on this? best, Namit

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quick note of thanks
by Chris Dagdigian 13 Oct '14

13 Oct '14

Wanted to send Dannon & the list a quick note of thanks. Cloudman-managed Galaxy is pretty slick. I'm using it today to run 26 individual Galaxy instances running on big c3.8xlarge AWS nodes for a training class. Each of the 26 training systems is built from a shared cluster string config which means I can stand up tested systems that also contain a "hidden" history that students can access and refer to if they get stuck. We wanted to give each student their own individual Galaxy sandbox to play on and Cloudman made it very easy. Faster than custom configuring a personal AMI and using Chef/devOps tricks to clone and automate the deployment. All told it took me about 1.5 days to get my head around cloudman and make all the usual mistakes regarding breaking things, screwing things up and otherwise running through the learning curve. After that it took me about 1 day to load the master cluster image up with data, history and run through all of the lab exercises. After that it was about 2 hours to share the cluster and start firing up the clones One thing that would help (and perhaps this is something that I missed in the documentation) would be the ability to pass in the shared cluster string as user-data at launch time. That would have let me fire up the training nodes with a single shell script. Instead I used a shell script to fire up the nodes but then I had to hit the cloudman URL on each node to punch in the shared-cluster URI string. Thanks again! Regards, Chris

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API : Max retries exceeded
by Gildas Le Corguille 13 Oct '14

13 Oct '14

Hi, I wrote a script which need to retrieve a list of all users on our production instance. It seems that we have too many users (325) :P bioblend.galaxy.client.ConnectionError: HTTPConnectionPool(host='galaxy.sb-roscoff.fr', port=8080): Max retries exceeded with url: /api/users?key=fd420zefff9a9df586210fd8c8452d98 (Caused by <class 'socket.error'>: [Errno 111] Connection refused): None My script is running on an test instance which have less users. Is there a way to set this threshold ? Thanks Gildas PS : don't try my api_key, little hacker, it's a fake :P

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GATK2 java version related issues
by Iry Witham 10 Oct '14

10 Oct '14

Hi Team, I am sorry to be a pest, but I am under-the-gun to get this resolved. I have followed the instructions for installing GATK2 on my cloud VM. After doing that I discovered that the version of java running on the VM was v1.6.x and GATK2 required v1.7.0x. I removed version 6 and installed version 7, uninstalled GATK2 and reinstalled it and reset all of the settings that may have reverted with the uninstalls/reinstalls. Now when I run Unified Genotyper I get the following error: Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:643) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) at java.net.URLClassLoader.access$000(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:212) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) Could not find the main class: org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit. Researching this I found a post at http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-tes… that refers to upgrading java as the solution. However, that did not fix the issue. In addition I copied the jar file to a temp directory and unzipped it to examine the MANAFEST.MF file for versioning issues. This is what I found: Manifest-Version: 1.0 Build-Jdk: 1.7.0_51 Built-By: gsa-engineering Created-By: Apache Maven Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK Archiver-Version: Plexus Archiver This tells me that there is something else causing the problem. Does anyone have an idea where to look now? Regards,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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Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc client?
by Chris Dagdigian 10 Oct '14

10 Oct '14

Just a paranoia check ... I manually started the cloudman galaxy AMI (ami-a7dbf6ce) and noticed that it is configured and running a boinc client Just wanted to check if this was legit and expected ... Regards, Chris

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Anyone else having issues with cloudman cloudlaunch?
by Chris Dagdigian 10 Oct '14

10 Oct '14

Anyone else having issues using cloudman version of galaxy? No matter what set of AWS keys I use to try to start a new galaxy cluster I always get the vague "Bad Request : Instance failure, but no specific error was detected. Please check your AWS Console." ... error on the launch screen. Nothing obvious in the AWS console. I'm using both my root AWS keys as well as IAM generated keys with full admin rights and no love. I do have one running cluster; does that need to be stopped or paused before I try to launch more? Regards, Chris

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Tool development: Is it possible to pass a user's id in dynamic_options() parameter?
by Dooley, Damion 10 Oct '14

10 Oct '14

This was asked a few years ago but no takers: Galaxy Tool Development: (http://dev.list.galaxyproject.org/Reading-user-id-before-the-execution-of-t…) Seems like this isn't possible, unless there's a way to plant user's name in a text field on the tool's form, so that a dynamic_options() call can refer to it? Thx for insights, Damion

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Is it possible to condition tool wrappers on external inputs?
by Melissa Cline 10 Oct '14

10 Oct '14

Hi Folks, I suspect I know the answer to this question already, but I have to ask just for the sake of completeness... I'm working on a tool for which I'd like to query an external server for the set of expected inputs, and then make that set available as input options. The tool in question will import a Galaxy dataset into an external cancer genomics database. The user will need to specify what cancer cohort the new data belongs under. In the perfect world, I would query this cancer genomics database for the existing cancer cohorts, and use that set of cohorts to populate the set of options for a select-type input parameter. Is anything like this possible? If so, where could I look at some examples? If not, is there anything you can think of to produce similar behavior? Thanks! Melissa

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Data uploaded with new upload tool doesn't get added to history
by Peter van Heusden 10 Oct '14

10 Oct '14

Hey there Using the new upload tool my data uploads but never appears in the history. All I can see in paster.log when I do an upload is: 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] "POST /tool_runner/index HTTP/1.0" 200 - "https://phillipl.sanbi.ac.za/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] "GET /api/histories/f597429621d6eb2b/contents HTTP/1.0" 200 - "https://phillipl.sanbi.ac.za/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] "GET /api/histories/f597429621d6eb2b HTTP/1.0" 200 - "https://phillipl.sanbi.ac.za/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" No errors in the javascript console, and this happens with both Chrome and Firefox (on Linux), code is latest galaxy-central. Any ideas where to debug? Thanks, Peter

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SQLalchemy InvalidRequestError
by Ulf Schaefer 09 Oct '14

09 Oct '14

Dear all Maybe one of you can shed some light on this error message that I see in the log file for one of my handler processes. I get about one of them per second. The effect is that most of the jobs remain in the "waiting to run" stage. The postgres database is running on a separate server and appear to be doing just fine. Any help is greatly appreciated. Thanks Ulf --- galaxy.jobs.handler ERROR 2014-10-07 10:32:24,676 Exception in monitor_step Traceback (most recent call last): File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py", line 161, in __monitor self.__monitor_step() File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py", line 184, in __monitor_step hda_not_ready = self.sa_session.query(model.Job.id).enable_eagerloads(False) \ File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1088, in query return self._query_cls(entities, self, **kwargs) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 108, in __init__ self._set_entities(entities) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 117, in _set_entities self._setup_aliasizers(self._entities) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 132, in _setup_aliasizers _entity_info(entity) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/util.py", line 578, in _entity_info mapperlib.configure_mappers() File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2260, in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined. --- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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