- galaxy-dev - lists.galaxyproject.org

pdb prompt under galaxy testing
by WANGYi 01 Sep '10

01 Sep '10

Hi Galaxy dev team, This is Yi WANG, developer from a team aiming to integrate some own tools into Galaxy framework for the tools' web application. We have finished the tool configs and are currently testing our tools under Galaxy testing framework. Sometimes when there are some exceptions raised during the tests, we would like to debug into our tool codes to see what had happed in detail. And we use python debug 'pdb' for this purpose. But when a breakpoint is reached during the test, we expect but are not able to see any pdb prompt (debug interface) or debug information from the console (although we are sure that the testing does pause for the break point), which makes the debug procedure rather difficult. And still, it is weird that, after we type "quit" command to exit pdb (the testing will of course resume), the log of the testing will then display the debug information which should have appeared previously under 'pdb' prompt. Could you please give us some hints on this? Any advice on this issue will be really appreciated. Thanks so much. Regards Yi WANG

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Adding Libraries
by Tanguy Le Carrour 01 Sep '10

01 Sep '10

Hello! I've a running instance of Galaxy that works just fine, thanks to Nate Coraor. I would like to add all the files that our centre produces, which is a lot, to the data library, and I would like to automate it. As I see it, there are 3 options: - add the data directly to the database (dataset, library, library_dataset...), but it "may not be" the best choice... - use the upload1 tool, but I need to first create a dataset (there is a dataset reference in the json configuration file isn't it?) - POST my "multiport/form-data" data to "/library_common/upload_library_dataset", but the library_id and folder_id are not the real ids and I haven't found out, yet, where they are coming from! I could really use a advice on which option is the best. Thank you in advance for your help! Best regards, Tanguy LE CARROUR -- Tanguy LE CARROUR Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

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Galaxy Genome Builds
by Anton Nekrutenko 31 Aug '10

31 Aug '10

Dear Galaxy user: Below are two important points about Galaxy genome builds that may affect your analysis results: 1. Canonical and Complete builds Many genomes provided by Galaxy originate from UCSC and are represented by a mix of canonical chromosomes (such as 1 through Y in mammals), mitochontrial genome (chrM), and unplaced fragments (chrUn) and/or haploblocks. Until last week we were using only canonical chromosomes and the mitochondrion to build indices required by NGS mappers (bwa, bowtie, bfast, lastz, and perm) and SAM Tools. However, for some analyses it is necessary to include regions that are not placed within the canonical chromosome set. Starting next week we will be providing two sets of NGS mapper indices: canonical (chr1 through chrY + chrM) and full (everything). A separate message will be sent out once this is enabled. 2. A recent un-announced change to hg19 The hg19 version of NGS and SAMTools indices contained only CANONICAL chromosomes (chr1 through Y + chrM) until August 20. On August 20 it was changed to the full version. As a result mapping jobs that were run after August 20, 2010 may return slightly different results. Anton Nekrutenko http://usegalaxy.org

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galaxy user quotas?
by lentaing＠jimmy.harvard.edu 30 Aug '10

30 Aug '10

Hi, We would like to enforce a policy of setting user disk quotas to a maximum of 10GB/user on our galaxy instance. Is there a way to specify this in galaxy, e.g. in universe.ini? If it's not currently implemented, could you point me to some relevant locations in the galaxy source to help me get started? Thanks, Len Cistrome Development Team

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links in param tags
by Belinda M. Giardine 27 Aug '10

27 Aug '10

Is it possible to include a link in the help attribute of the param tag set? Belinda

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request_param_translation and request_param
by Erick Antezana 27 Aug '10

27 Aug '10

Hi, I've got some questions regarding some tags (e.g. request_param_translation and request_param). Their doc is fully described here: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax 1. In the doc of 'request_param_translation', we find: "This tag set is contained within the <param> tag set - it contains a set of <request_param> tags." But it seems that it is not needed to include this tag set within the 'param' one (but directly child of the 'tool' tag)? 2. in the doc of 'request_param', there is a nice table with the attributes, values, etc. Is the value "URL_method" missing in that table as possible value? if so, what would be the difference between that definition and the one we set in the 'tool' tag? Is the list of possible values a comprehensive one? 3. The example of usage of 'request_param_tranlsation' has a typo: "requst_param_translation" instead of "request_param_translation". I guess that the suffixing "}" in the remote_name example (in the request_param table) should also be deleted? 4. is there any doc about the 'uihints' tag? (found in some examples such as ucsc_tablebrowser.xml). cheers, Erick

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Re: [galaxy-dev] [galaxy-bugs] AMI image
by Enis Afgan 26 Aug '10

26 Aug '10

Hi Loretta, Our AMI is hosted on Amazon as an EBS AMI so it is not possible to download it in its entirety. If you plan on using it on AWS, it is publicly available so you can use it or tweak it as desired. The EBS snapshot from which this AMI is derived is also publicly available as snap-d0a071b8. If you need to replicate the services/functionality included on this AMI outside AWS, we have a script that defines and automates the process of building the machine image using Python Fabric. The source code (with instructions on how to use it) is in the following repository: http://bitbucket.org/afgane/mi-deployment. Hope this helps, Enis > Hi, > > This is really a request... We have a cloud implementation and I was > wondering if you have or can make your AMI image (AMI: ami-ed03ed84) > available for download... > > Thanks... > > -Loretta > > *********************** > Loretta Auvil > lauvil(a)illinois.edu > 1205 W. Clark St, MC-257 > Urbana, IL 61801 > 217-265-8021 > > > > > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs >

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Downloading datasets
by SHAUN WEBB 26 Aug '10

26 Aug '10

Hi, I've noticed that when I try to save a large history dataset from history (e.g SAM file with 17 million lines) that memory usage by the python process running Galaxy increases dramatically, sometimes to the point of crashing my server. Even after the file has been saved to my machine the memory usage is maintained. Is there any way to clear this? Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [galaxy-dev] [galaxy-user] finding file format of data item
by Jeremy Goecks 26 Aug '10

26 Aug '10

>> >> I have a tool that can be run on multiple data formats. But I need to run it differently depending on the format of the input dataset. How can I get the input data format? >> >> In the tools .xml file I have: >> >> <param format="interval,lped" name="input1" type="data" label="SNPs"> >> >> and >> >> #if $input1.metadata.format=="interval" ... >> >> The if doesn't work, what should be there? Hi Belinda, The condition you want to use is this: #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('interval').__class__): You can see this example in context by looking at the XML tool definition file for the intersect tool, intersect.xml Let us know if this doesn't solve your problem. Best, J.

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GMOD Europe 2010 Update
by Dave Clements, GMOD Help Desk 25 Aug '10

25 Aug '10

Hello all, GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts in less than two weeks. If you are planning on attending and haven't yet registered, then please do so in the next few days. The BioMart Workshop has only a few slots left, and the registration fee for the GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging people to submit topic suggestions for the GMOD Meeting and the GMOD Satellite Meetings. We are also pleased to announce that Jason Swedlow of the University of Dundee will be the guest speaker at the GMOD Meeting. Jason will speak on "The Open Microscopy Environment: Open Informatics for Biological Imaging," a particularly timely topic as many researchers move into image intensive areas such as phenotypes and gene expression, and as high-throughput imaging platforms become available. There is still space available at all 4 events, and registration for the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop is free. Scott Cain and Dave Clements Links: http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/September_2010_GMOD_Meeting http://gmod.org/wiki/Satellite_Meetings_-_GMOD_Europe_2010 http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010 http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010

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