- galaxy-dev - lists.galaxyproject.org

tool form in remote mode
by Yanbo Ye 28 Apr '14

28 Apr '14

Hi, Galaxy Developers, I'm trying to integrate galaxy into another system and using its remote mode. While I still want to use the html of the tool form generated by galaxy. I know that I cannot get the html through the API. So I want to write some code to call the tool package code directly. But I can't find the documentation about the tool package and don't know where to start with. Can any one help me? Any help will be appreciated! Best, Yanbo

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user account
by Jun Fan 26 Apr '14

26 Apr '14

Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for "operations.append" and "item.deleted" and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make "delete user" function available in the UI as Nate suggested. Any guidance? Best regards! Jun

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how to edit the workflow (the connection between Select Variants and SnpEff)
by Wang, Xiaofei 25 Apr '14

25 Apr '14

Dear there, I tried to edit the CloudMap EMS workflow based on my own data. But I failed to make a connection between "Select Variants" and "SnpEff". In fact, I failed to reconstruct the connection between them even when I removed the original one by clicking "x" when moved cursor on the line. The arrow on left of SnpEff does not become green when I drugged the line from output_vcf(vcf) to it after I moved the original one. Could you tell me why does this happen and how should I figure this out? [cid:d1b6886a-ce80-e25c-2ede-e7afbe43263c] Thanks a lot! Best Xiaofei

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Limits for enumerate for multiple input files
by Ulf Schaefer 25 Apr '14

25 Apr '14

Dear all I am using this control to allow the user to input multiple files: <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" /> and I am using this for loop in the cheetah code to access the control: <command interpreter="bash"> script.sh ... #for $i, $input_vcf in enumerate( $input_vcfs ): "${input_vcf}", #end for </command> It appears that when a user selects many files (25 in this case) the bash command in the command tag never gets executed. Therefore the job is never queued. The history item shows 'Waiting to run' indefinitely. Calling the script.sh manually with 25 input files works fine. Any hint as to how to debug this would be greatly appreciated. Thanks a lot Ulf ************************************************************************** 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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"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
by Jennifer Jackson 25 Apr '14

25 Apr '14

Hello Sarah, This commit was made some time ago and is already in the distribution. Are you running the latest distribution? And you have uncommented the configuration line for this in your universe.wgsi.ini file? # Directory where chrom len files are kept, currently mainly used by trackster #len_file_path = tool-data/shared/ucsc/chrom <--- here Upgrade and adjust the file as needed. https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution I am going to forward this over to the galaxy-dev(a)bx.psu.edu mailing list for further troubleshooting, should this not resolve the problem. Please keep all replies on that list. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists *Galaxy Biostar is replacing the galaxy-user mailing list! /Update now! /** ** Here's how ->>> https://wiki.galaxyproject.org/Support/Biostar** * On 4/22/14 3:25 AM, Sarah Maman wrote: > Hello, > > I try to use "Intersect multiple sorted BED files" tool without success. > A genome_test have been added in galaxy (genome_test.len in > galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc > fils in tool-data/) but "Intersect multiple sorted BED files" gives > this error message : > An error occurred running this job: /Epilog : job finished at lun. > mars 24 15:55:04 CET 2014 > Error: The requested genome file > (/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could > not be opened. Exiting! > > So, /I have integrated the code modification submitted in Galaxy > Central > (https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a371…) > - chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) > + chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) > > But I always have the same error message. > > Could you please help us ? > Thanks in advance, > Sarah > > -- > --*-- > Sarah Maman > INRA - GenPhySE - SIGENAE > http://www.sigenae.org/ > Chemin de Borde-Rouge - Auzeville - BP 52627 > 31326 Castanet-Tolosan cedex - FRANCE > Tel: +33(0)5.61.28.57.08 > Fax: +33(0)5.61.28.57.53 > --*-- > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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problem with output file
by Clement Lionnet 25 Apr '14

25 Apr '14

Hi, I would like to devellop a wrapper with the script EMIRGE. I have a problem with output file because the script creates one folder which containt other folder and i would like to save all folder and get back two file containt in the last folder. My wrapper create folder but at the end my dataset show an error and I don't now why.

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DRMAA configuring issue
by Hakeem Almabrazi 25 Apr '14

25 Apr '14

Hi, I am trying to get DRMAA runner working for my local galaxy cluster. However, I am having hard time configuring it my system. So far, I have installed Torque 2.5.12 and it seems to work as expected. I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH galaxy_env)galaxy@GalaxyTest01[/home/galaxy/galaxy-dist]$ echo $DRMAA_LIBRARY_PATH /usr/local/lib/libdrmaa.so My job.conf.xml <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <handlers default="handlers"> <handler id="main" tags="handlers"/> </handlers> <destinations default="sge_default"> <destination id="sge_default" runner="drmaa"/> </destinations> </job_conf> This is the error I am getting when I start galaxy. galaxy.jobs INFO 2014-04-21 15:37:30,730 Handler 'main' will load all configured runner plugins Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 130, in __init__ self.job_manager = manager.JobManager( self ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 30, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 568, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 489, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__ self.ds.initialize() File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", line 274, in initialize _w.init(contactString) File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/wrappers.py", line 59, in init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/home/galaxy/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) DrmCommunicationException: code 2: (null) Removing PID file paster.pid I am not sure what is the issue here or how to go about resolving it. I will really appreciate it if someone can tell me how to debug it? Best regards Hak

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Character encoding on the command line
by Jim McCusker 25 Apr '14

25 Apr '14

When I pass a parameter on the command line certain characters (like @) are transformed to X+hexadecimal. Is this some sort of sanitization step? Would using a config file ( https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cconfigfile.…) avoid that sort of mess? I'm not sure I've seen this documented (I could be wrong though). Thanks, Jim

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Galaxy/Cloudman Compute Nodes User
by Jim McCusker 25 Apr '14

25 Apr '14

Hi all, I need to add a .boto file to the user that galaxy jobs get exec'ed as on cloudman nodes. I thought it would copy over what the galaxy server has in its home directory, but that doesn't seem to happen. How can I get things like my .boto file to migrate over to new cloudman nodes when they are spun up? Thanks, Jim

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Re: [galaxy-dev] A proposed modules extension for toolshed wrappers
by Guest, Simon 25 Apr '14

25 Apr '14

Just been reading a bit more about the Galaxy packaging system. Here's a slight modification to what I was suggesting that might fit in a bit better. Apologies for not being more familiar with the existing system before proposing extensions. Recall that my goal is to support using a system-installed (native) package, at a defined version, which I aim to achieve by loading the appropriate environment module before running a tool. We still have tool_dependencies.xml defining a package at a particular version, but rather than download and build the source code, there's just a directive that says how to pick up the correct program version at runtime, e.g. which environment module to load. So instead of the tool_dependencies.xml fragment: <tool_dependency> <package name="bwa" version="0.6.2"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2</action> <action type="shell_command">make</action> <action type="move_file"> <source>bwa</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> </tool_dependency> We have something like this (NB: element and attribute names are for illustrative purposes only): <tool_dependency> <package name="bwa" version="0.6.2"> <use_native> <actions> <action type="module_load">bwa/0.6.2</action> </actions> </use_native> </package> </tool_dependency> This causes the right thing (module load bwa/0.6.2) to be stuck into the dependencies env.sh file when this package is installed from the toolshed. We could call this toolshed tool native_package_bwa_0_6_2, to avoid confusion with the existing download-and-make one. We might want a bit of flexibility on what actions are supported (in case we want to support Software Collections, for example). What do you think? cheers, Simon PS: In case it wasn't already clear, solving this problem well is quite important to us here at AgResearch. ;-) ======================================================================= 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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