galaxy-dev September 2014

galaxy-dev@lists.galaxyproject.org

59 participants
76 discussions

Question about Terms and Conditions for public galaxy server under development
by audrey michel 29 Sep '14

29 Sep '14

Hi, We are developing a galaxy server for public usage and we would like to know if we should use the same terms and conditions as you provide for Galaxy main when we publicly launch our server: https://usegalaxy.org/static/terms.html If so, could you let us know if we can use the exact same text or if we need to replace "The Pennsylvania State University" with our University name? If we can't use the text in the link above, could you provide recommendations? Kind Regards, Audrey Michel

2 1

bwa and bwa-mem wrappers...
by Anton Nekrutenko 29 Sep '14

29 Sep '14

...have been committed to toolshed: https://toolshed.g2.bx.psu.edu/view/devteam/bwa_0_7_10 and github: https://github.com/nekrut/bwa-mem any feedback (especially in the form of github pull requests) is appreciated. One of the main changes is that these tools have no helper python scripts (all magic happens within the tool xml) and they produce BAM output. a. -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology *http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>* (814) 826-3051

1 0

Set a new metadata attribute
by Nikos Sidiropoulos 29 Sep '14

29 Sep '14

Hi all, In a tool that I am writting I want to pass an input parameter value (string) into the output file's metadata. Meaning that one of the tool parameters is a barcode signature, 'NNWTGXN' for example. I want that attribute to be stored somehow in the output file in order to be read by a subsequent tool without the user having to set that parameter again. The files I'll be working with are in FASTQ, BAM and tabular format. Is it possible? Bests, Nikos

3 2

Cloudman installed tools missing referneces
by Iry Witham 26 Sep '14

26 Sep '14

Hi Team, I have a new instance of galaxy cloudman running on AWS and when I go to run some of the tools I have installed like SAM-to-BAM it requires a reference genome, but none is available. This is SAM-to-BAM version 1.1.4. This is the first tool I have found this to be an issue so far. Is there a loc file that needs modification? I will need to add several references. Thanks, 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.

1 0

tool for STAR RNA-seq aligner
by David Hoover 26 Sep '14

26 Sep '14

Hi, I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I realize I may be reinventing another wheel. Has anyone else created a tool for STAR? There's nothing else in the toolsheds for it yet. David -------------------- David Hoover, PhD Helix Systems Staff SCB/DCSS/CIT/NIH 301-435-2986 http://helix.nih.gov

5 11

sendmail from addr
by Evan Bollig 25 Sep '14

25 Sep '14

On a local instance of Galaxy, I get this error when attempting to reset my password: Failed to reset password: (501, '5.1.7 Bad sender address syntax', 'galaxy-no-reply(a)10.32.16.121') I am told my mail server requires the from address to either have a domain name, or the IP address to be in brackets (e.g., [10.32.16.121]). Is there an option to configure the from address format, or override the address? If there are no configuration options, what files would I need to modify to add brackets? The domain name is not an option. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

2 1

Question re: email alerts on workflow errors
by Evan Bollig 25 Sep '14

25 Sep '14

When I run a workflow and multiple steps fail, does Galaxy have the option to send a digest of all problems, or does each failed step result in another email? Or maybe only the first failed task results in an email alert? I'm trying not to get spammed when a workflow fails. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

2 1

Error report via API?
by Evan Bollig 25 Sep '14

25 Sep '14

Is there an API endpoint for sending the error report for a failed step in a history? I would like to run a workflow via API and email the first error that occurs. -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

2 1

DRMAA Slurm error
by Pardo Diaz, Alfonso 25 Sep '14

25 Sep '14

Hi, I have configured a new galaxy-project site with SLURM (version 14). I have one server with a Galaxy-Project instance, one node with SLURM server and two SLURM worker nodes. I have compile SLURM-DRMAA from source codes. When I run “drmaa-run /bin/hostname” it’s work. But, when I try to run the server I got the next error: Traceback (most recent call last): File "/home/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy-dist/lib/galaxy/app.py", line 141, in __init__ self.job_manager = manager.JobManager( self ) File "/home/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 32, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 704, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/galaxy-dist/lib/galaxy/jobs/__init__.py", line 621, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/home/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__ self.ds.initialize() File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/session.py", line 257, in initialize py_drmaa_init(contactString) File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/wrappers.py", line 73, in py_drmaa_init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) AlreadyActiveSessionException: code 11: DRMAA session already exist. [root@galaxy-project galaxy-dist]# This is my “job_conf.xml”: <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner"> <param id="drmaa_library_path">/usr/local/lib/libdrmaa.so</param> </plugin> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="drmaa_slurm"> <destination id="local" runner="local"/> <destination id="multicore_local" runner="local"> <param id="local_slots">4</param> <param id="embed_metadata_in_job">True</param> <job_metrics /> </destination> <destination id="docker_local" runner="local"> <param id="docker_enabled">true</param> </destination> <destination id="drmaa_slurm" runner="drmaa"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="direct_slurm" runner="slurm"> <param id="nativeSpecification">--time=00:01:00</param> </destination> </destinations> <resources default="default"> <group id="default"></group> <group id="memoryonly">memory</group> <group id="all">processors,memory,time,project</group> </resources> <tools> <tool id="foo" handler="trackster_handler"> <param id="source">trackster</param> </tool> <tool id="bar" destination="dynamic"/> <tool id="longbar" destination="dynamic" resources="all" /> <tool id="baz" handler="special_handlers" destination="bigmem"/> </tools> <limits> <limit type="registered_user_concurrent_jobs">2</limit> <limit type="anonymous_user_concurrent_jobs">1</limit> <limit type="destination_user_concurrent_jobs" id="local">1</limit> <limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit> <limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit> <limit type="destination_total_concurrent_jobs" id="local">16</limit> <limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit> <limit type="walltime">24:00:00</limit> <limit type="output_size">10GB</limit> </limits> </job_conf> Can you help me? I am newbie with “Galaxy Project” administration. THANKS IN ADVANCE!!!! Alfonso Pardo Diaz System Administrator / Researcher c/ Sola nº 1; 10200 Trujillo, ESPAÑA Tel: +34 927 65 93 17 Fax: +34 927 32 32 37 [CETA-Ciemat logo]<http://www.ceta-ciemat.es/> ---------------------------- Confidencialidad: Este mensaje y sus ficheros adjuntos se dirige exclusivamente a su destinatario y puede contener información privilegiada o confidencial. Si no es vd. el destinatario indicado, queda notificado de que la utilización, divulgación y/o copia sin autorización está prohibida en virtud de la legislación vigente. Si ha recibido este mensaje por error, le rogamos que nos lo comunique inmediatamente respondiendo al mensaje y proceda a su destrucción. Disclaimer: This message and its attached files is intended exclusively for its recipients and may contain confidential information. If you received this e-mail in error you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited and may be unlawful. In this case, please notify us by a reply and delete this email and its contents immediately. ----------------------------

1 1

Uploading .vcf files
by Katherine Collins 24 Sep '14

24 Sep '14

Hi, I am attempting to upload 94 .vcf files (only about 20 kb each). However, the Files have been gray (file waiting to run) for a few hours. Then, I received the following message: An error occurred while getting updates from the server. Please contact a Galaxy administrator if problem persists. With a link "details" that included the message below. Thank you for any information that you may be able to offer. I am using the "main" usegalaxy.org Best, Katie Collins User name: Khofer E-mail : khofer(a)buffalo.edu { "agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1", "url": "https://usegalaxy.org/api/histories/df50bec76aaef863/contents", "data": "", "options": { "data": {}, "parse": true, "emulateHTTP": false, "emulateJSON": false }, "xhr": { "readyState": 4, "responseText": "\n <!DOCTYPE HTML>\n <html>\n <head>\n <style type=\"text/css\">\n body { color: #303030; background: #dfe5f9; font-family:\"Lucida Grande\",verdana,arial,helvetica,sans-serif; font-size:12px; line-height:16px; }\n .content { max-width: 720px; margin: auto; margin-top: 50px; }\n </style>\n <title>Internal Server Error</title>\n \n </head>\n <body>\n <div class=\"content\">\n <h1>Internal Server Error</h1>\n\n <h2>Galaxy was unable to successfully complete your request</h2>\n\n <p>\n An error occurred.\n </p>\n\n This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.\n\n <p><b>The error has been logged to our team.</b> If you want to contact us about this error, please reference the following<br><br><b><large>GURU MEDITATION: #66dc77d38914442e886df33114ef1ece</large></b></p>\n </div>\n </body>\n </html>", "status": 500, "statusText": "Internal Server Error", "responseHeaders": { "Date": "Wed, 24 Sep 2014 16:29:43 GMT\r", "Transfer-Encoding": "Identity\r", "Connection": "keep-alive\r", "Server": "nginx/1.4.7\r", "Content-Type": "text/html\r" } }, "source": [ { "deleted": true, "history_id": "df50bec76aaef863", "visible": true, "hid": 1, "id": "bbd44e69cb8906b55413f473fd4ce3b1", "history_content_type": "dataset", "name": "Brighmania-isignis_S1Var.flt.vcf", "resubmitted": false, "url": "/api/histories/df50bec76aaef863/contents/datasets/bbd44e69cb8906b55413f473fd4ce3b1", "state": "queued", "type": "file", "purged": true, "type_id": 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galaxy-dev September 2014