February 2012 - galaxy-dev - lists.galaxyproject.org

Condor in bioinformatics pipeline
by Jennifer Jackson 14 Feb '12

14 Feb '12

Hi Nathan, I am going to move your question over to the galaxy-dev(a)bx.psu.edu mailing list to see if anyone in the development community has feedback. Galaxy-user is mostly a Q & A list for scientists working with tools on the main Galaxy public server. http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists Thanks! Jen Galaxy team On 2/3/12 7:21 AM, Nathan Panike wrote: > Has anyone had success using the Condor scheduling system with the > following software? > > RSEM > ChimeraScan > GATK > BreakDancer > VariationHunter > > Thanks, > > Nathan Panike, nwp(a)cs.wisc.edu > UW-Madison Center for High Throughput Computing > ___________________________________________________________ > 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Re: [galaxy-dev] Problems with custom data types and sniffers in shed tools
by Greg Von Kuster 14 Feb '12

14 Feb '12

Hello Ira, Very sorry for the back-and-forth on this. The behavior you encountered was accurate - the environment in which I was testing was not pristine. I have committed a fix for this issue in revision b4ba8b20d78d, which is now available from our central repo. I started looking at changing things so that proprietary sniffers are loaded before the sniffers defined in the Galaxy distribution, and determined that this will be a bit non-trivial. Problems arise due to potential conflicts between a proprietary datatype that has the same extension as a datatype defined in the Galaxy distribution. The approach I've taken to deal with this is that datatypes in the Galaxy distribution get loaded first, and then any conflicting proprietary datatypes will be ignored. Loading proprietary datatypes first will not allow for this rule. I'll gladly listen to advice from the community on this, but in the meantime, proprietary datatypes and sniffers are loaded after those in the distribution. Thanks for your patience and help on this issue. Greg On Feb 6, 2012, at 11:37 PM, Ira Cooke wrote: > Hi Greg, > > As far as I know there is nothing in my local setup that affects this. As I test I did the following; > > Checked out a clean copy of galaxy-central > Edited my universe_wsgi.ini as follows; > - Changed the port to 8300 > - Added an admin user > - Uncommented this line > tool_config_file = tool_conf.xml,shed_tool_conf.xml > > Edited shed_tool_conf.xml to point to ../shed_tools_galaxy_central (which is an empty directory) > > Started up galaxy > ./run.sh --reload > > I then went straight to admin -> "Search and browse tool sheds" and selected the main galaxy toolshed. > I then selected the gmap tool and told it to install. My paster log is at the bottom of this mail. > > My system is Mac OSX 10.7.2 and I'm running python 2.7.1 > > I then went to the relevant bit of code and inserted some print statements. I found that; > > On line 191 in registry.py there is; > > module = __import__( datatype_module ) > > and the value of datatype_module is galaxy.datatypes.gmap > > this line seems to be causing the exception ... I'm not a python programmer so I don't really know how module importing works ... could this be related to the version of python I'm running? > alternatively should the "imported_modules" variable be used here .. since wouldn't galaxy.datatypes.gmap suggest that the module needs to be located inside the main galaxy lib rather than in the shed_tools. > > Strange that I'm the only one who gets these errors? Any ideas what it could be? > > Ira > > > -- paster log -- > > Cloning http://toolshed.g2.bx.psu.edu/repos/jjohnson/gmap > destination directory: gmap > requesting all changes > adding changesets > adding manifests > adding file changes > added 11 changesets with 32 changes to 17 files > updating to branch default > resolving manifests > getting README > getting gmap.xml > getting gmap_build.xml > getting gsnap.xml > getting iit_store.xml > getting lib/galaxy/datatypes/gmap.py > getting snpindex.xml > getting tool-data/datatypes_conf.xml > getting tool-data/gmap_indices.loc.sample > 9 files updated, 0 files merged, 0 files removed, 0 files unresolved > galaxy.util.shed_util DEBUG 2012-02-07 14:25:35,100 Updating cloned repository to revision "93911bac43da" > resolving manifests > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > docutils WARNING 2012-02-07 14:25:35,512 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. > > galaxy.util.shed_util DEBUG 2012-02-07 14:25:35,589 Adding new row (or updating an existing row) for repository 'gmap' in the tool_shed_repository table. > docutils WARNING 2012-02-07 14:25:35,701 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. > > docutils WARNING 2012-02-07 14:25:35,863 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. > > galaxy.tools DEBUG 2012-02-07 14:25:35,932 Reloading section: gmap > galaxy.tools DEBUG 2012-02-07 14:25:35,997 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap/2.0.1, version: 2.0.1. > galaxy.tools DEBUG 2012-02-07 14:25:36,026 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_build/2.0.0, version: 2.0.0. > docutils WARNING 2012-02-07 14:25:36,077 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. > > galaxy.tools DEBUG 2012-02-07 14:25:36,103 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gsnap/2.0.1, version: 2.0.1. > galaxy.tools DEBUG 2012-02-07 14:25:36,268 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_iit_store/2.0.0, version: 2.0.0. > galaxy.tools DEBUG 2012-02-07 14:25:36,316 Loaded tool id: toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_snpindex/2.0.0, version: 2.0.0. > galaxy.datatypes.registry DEBUG 2012-02-07 14:25:38,608 Loading datatypes from /Users/iracooke/Sources/shed_tools_galaxy_central/toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/93911bac43da/gmap/tool-data/datatypes_conf.xml > galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,609 Error appending sniffer for datatype galaxy.datatypes.gmap:IntervalAnnotation to sniff_order: No module named gmap > galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,609 Error appending sniffer for datatype galaxy.datatypes.gmap:SpliceSiteAnnotation to sniff_order: No module named gmap > galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,610 Error appending sniffer for datatype galaxy.datatypes.gmap:IntronAnnotation to sniff_order: No module named gmap > galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,610 Error appending sniffer for datatype galaxy.datatypes.gmap:SNPAnnotation to sniff_order: No module named gmap > > > > > On 07/02/2012, at 3:05 AM, Greg Von Kuster wrote: > >> Hello Ira, >> >> I believe proprietary datatype sniffers included in tool shed repositories are loading as expected - at least I cannot reproduce the behavior you are seeing. The datatypes_conf.xml file included in the latest revision of the gmap repository on the main Galaxy tool shed looks like this: >> >> <?xml version="1.0"?> >> <datatypes> >> <datatype_files> >> <datatype_file name="gmap.py"/> >> </datatype_files> >> <registration> >> <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> >> <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> >> <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> >> <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> >> <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> >> <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> >> <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> >> <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> >> <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> >> <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> >> </registration> >> <sniffers> >> <sniffer type="galaxy.datatypes.gmap:IntervalAnnotation"/> >> <sniffer type="galaxy.datatypes.gmap:SpliceSiteAnnotation"/> >> <sniffer type="galaxy.datatypes.gmap:IntronAnnotation"/> >> <sniffer type="galaxy.datatypes.gmap:SNPAnnotation"/> >> </sniffers> >> </datatypes> >> >> Here is the snippet of my paster log when I install the gmap tool shed repository - notice that the tools, datatypes and sniffers are all loaded. I'm installing it from a local tool shed, but I downloaded the latest version from the main Galaxy tool shed and uploaded it with no changes to my local tool shed for testing. >> >> galaxy.web.controllers.admin_toolshed DEBUG 2012-02-06 10:50:33,686 Loading new tool panel section: gmap >> galaxy.util.shed_util DEBUG 2012-02-06 10:50:33,687 Installing repository 'gmap' >> galaxy.util.shed_util DEBUG 2012-02-06 10:50:33,687 Cloning http://test@gvk.bx.psu.edu:9009/repos/test/gmap >> destination directory: gmap >> requesting all changes >> adding changesets >> adding manifests >> adding file changes >> added 1 changesets with 10 changes to 10 files >> updating to branch default >> 10 files updated, 0 files merged, 0 files removed, 0 files unresolved >> galaxy.util.shed_util DEBUG 2012-02-06 10:50:34,062 Updating cloned repository to revision "dbcccd1e4dfd" >> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >> docutils WARNING 2012-02-06 10:50:34,388 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. >> >> galaxy.util.shed_util DEBUG 2012-02-06 10:50:34,437 Adding new row (or updating an existing row) for repository 'gmap' in the tool_shed_repository table. >> docutils WARNING 2012-02-06 10:50:34,533 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. >> >> docutils WARNING 2012-02-06 10:50:34,657 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. >> >> galaxy.tools DEBUG 2012-02-06 10:50:34,718 Reloading section: gmap >> galaxy.tools DEBUG 2012-02-06 10:50:34,769 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap/2.0.1, version: 2.0.1. >> galaxy.tools DEBUG 2012-02-06 10:50:34,813 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap_build/2.0.0, version: 2.0.0. >> docutils WARNING 2012-02-06 10:50:34,846 <string>:10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. >> >> galaxy.tools DEBUG 2012-02-06 10:50:34,877 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gsnap/2.0.1, version: 2.0.1. >> galaxy.tools DEBUG 2012-02-06 10:50:34,911 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap_iit_store/2.0.0, version: 2.0.0. >> galaxy.tools DEBUG 2012-02-06 10:50:34,962 Loaded tool id: gvk.bx.psu.edu:9009/repos/test/gmap/gmap_snpindex/2.0.0, version: 2.0.0. >> galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,147 Loading datatypes from /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gmap/dbcccd1e4dfd/gmap/gmap-93911bac43da/tool-data/datatypes_conf.xml >> galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,159 Loaded sniffer for datatype: galaxy.datatypes.gmap:IntervalAnnotation >> galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,160 Loaded sniffer for datatype: galaxy.datatypes.gmap:SpliceSiteAnnotation >> galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,161 Loaded sniffer for datatype: galaxy.datatypes.gmap:IntronAnnotation >> galaxy.datatypes.registry DEBUG 2012-02-06 10:50:35,161 Loaded sniffer for datatype: galaxy.datatypes.gmap:SNPAnnotation >> >> >> >> >> If I stop and restart my Galaxy server after I've installed the gmap repository, everything loads correctly as well: >> >> galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,713 Loading datatypes from ../shed_tools/gvk.bx.psu.edu/repos/test/gmap/dbcccd1e4dfd/gmap/gmap-93911bac43da/tool-data/datatypes_conf.xml >> galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,715 Loaded sniffer for datatype: galaxy.datatypes.gmap:IntervalAnnotation >> galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,715 Loaded sniffer for datatype: galaxy.datatypes.gmap:SpliceSiteAnnotation >> galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,716 Loaded sniffer for datatype: galaxy.datatypes.gmap:IntronAnnotation >> galaxy.datatypes.registry DEBUG 2012-02-06 10:57:10,716 Loaded sniffer for datatype: galaxy.datatypes.gmap:SNPAnnotation >> >> >> Have you made any changes to your local Galaxy instance that may have resulted in proprietary datatypes / sniffers not being loaded correctly? What version of the Galaxy distribution are you running? You should be at 6672:e38a9eb21336 from the central repository for the latest tool shed code. However, proprietary datatype support has not been touched in some time. >> >> >> On Feb 5, 2012, at 7:04 PM, Ira Cooke wrote: >> >>> Hi, >>> >>> We're developing a suite of galaxy tools for doing proteomics. As part of that we're developing a display application ( https://bitbucket.org/Andrew_Brock/proteomics-visualise ) for viewing pepXML and protXML files and we rely very heavily on custom datatypes. We've got this working in a fork of galaxy-dist ( https://bitbucket.org/iracooke/galaxy-proteomics ) but would love to be able to get rid of this fork and integrate all our customisations into a shed tool. >>> >>> I initially tried following the instructions here http://wiki.g2.bx.psu.edu/Tool%20Shed#Including_proprietary_data_types_that… and was able to successfully get my custom datatypes to load. Unfortunately though I could not get my sniffers to work. I think there are two reasons for this; >>> >>> The first problem is that it looks like the sniffers are never loaded. I get errors like this when the tool is loaded; >>> >>> galaxy.datatypes.registry DEBUG 2012-02-06 10:26:51,317 Loading datatypes from /Users/iracooke/Sources/shed_tools_galaxy_central/toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/93911bac43da/gmap/tool-data/datatypes_conf.xml >>> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,318 Error appending sniffer for datatype galaxy.datatypes.gmap:IntervalAnnotation to sniff_order: No module named gmap >>> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,319 Error appending sniffer for datatype galaxy.datatypes.gmap:SpliceSiteAnnotation to sniff_order: No module named gmap >>> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,319 Error appending sniffer for datatype galaxy.datatypes.gmap:IntronAnnotation to sniff_order: No module named gmap >>> galaxy.datatypes.registry WARNING 2012-02-06 10:26:51,319 Error appending sniffer for datatype galaxy.datatypes.gmap:SNPAnnotation to sniff_order: No module named gmap >>> >>> These errors aren't just restricted to my tool ... as you can see from the above they also occur in the gmap example installed from the main galaxy toolshed. >>> >>> I tried hacking the code in registration.py to get this to work ... it looks like the section where sniffers are loaded does not use the "imported_modules" variable. I was able to get this error message to go away, but I still don't get proper sniffer behaviour (eg when I click "Auto detect" when editing a dataset the dataset is set to a generic type). >>> >>> Another issue is that I would like the sniffers loaded from my shed_tool to be used by the "Upload" tool .. but if I look at the source for upload.py and upload.xml I see >>> >>> -- Upload.xml >>> <command interpreter="python"> >>> upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile >>> >>> --Upload.py >>> def __main__(): >>> >>> .... >>> >>> registry = Registry() >>> registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) >>> >>> which looks like the upload tool is not configured to use the custom datatypes available in shed tools. >>> >>> >>> Would it be possible to make the following changes; >>> >>> (a) Add custom sniffers to the sniff order when shed tools are loaded. Importantly since custom datatypes are usually quite specific I would suggest that these are loaded at the top of the sniff order? Or alternatively if a sniffer is for a datatype that descends from a superclass it should have priority over the parent class (since by definition it is more specific). >>> >>> (b) Change the upload tool so that it respects custom sniffers in shed tools. >>> >>> I guess that our case is a bit unusual in that we are trying to co-opt galaxy ( a genomics tool) to do proteomics ... so I understand that these changes might not be a priority. Nevertheless, if this could be done it would be fantastic for us as we could abandon our fork and have all our functionality included in a shed tool. >>> >>> >>> Regards >>> Ira >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >

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Uploading large file in browser
by Kim, Hyunsoo 14 Feb '12

14 Feb '12

Hello, I have local instance of galaxy and wanted to modify "upload file" so that I will be able to upload large files ( > 2GB). The reason I am trying to do this in browser is that extra tools for FTP do not really work in my environment because of all the constraints and firewalls. I came up with jQuery file upload tool (http://blueimp.github.com/jQuery-File-Upload/) and the tool seems fine if it is possible me to integrate into my galaxy instance. My questions are: -Is it too cumbersome to achieve this goal with external tools? -how deep should I hit the galaxy (at the code level) to integrate this jquery tool? -Are there any alternatives to upload large files in browser without FTP? Thanks, Daniel

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Re: [galaxy-dev] [galaxy-user] Result of annotation hg18 and hg19 on one file
by Dannon Baker 14 Feb '12

14 Feb '12

Hi, Based on your previous questions, I'm going to guess that you're trying to add multiple tools, run both on an input dataset in series, and see the results in the History. Is this the case? If you're referring to how to combine these into one process, take a look at the Galaxy workflow capabilities. In any event, if you could clarify what you're trying to accomplish I'm sure I can help out. Also, I've moved this question over to the galaxy-dev mailing list which should be used for anything development related, tools included. Thanks! -Dannon On Feb 13, 2012, at 1:25 PM, La Chi wrote: > Hi everyone, > how can i write the result of both functions in one single file then history panel will show its result.. > thanks > ___________________________________________________________ > 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/

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Re: [galaxy-dev] galaxy cloud help
by Dannon Baker 14 Feb '12

14 Feb '12

Sure, I'm happy to help, though in the future it's probably best to mail galaxy-dev (cc'd for ticket tracking) directly as there are several of us that may be able to answer and get a response out sooner. That said, your problem is likely due to a permissions issue with the new tool snapshot(snap-b28be9d5) created yesterday that I've fixed, it should work next time you start an instance. Let me know if this doesn't resolve things for you. Thanks! -Dannon On Feb 14, 2012, at 10:57 AM, brennac2(a)mskcc.org wrote: > I got your email from a [galaxy-dev] entry. Could I ask you for help with a cloud installation problem or could you point me to the best place to submit the question? I will describe the problem below but understand if you are not able to provide support. > > Thank you in advance, > > Cameron Brennan, MD > Human Oncology and Pathogenesis Program > Memorial Sloan-Kettering Cancer Center > New York > > Problem: > I have gotten Cloudman running on EC2 but the “Service Status” shows yellow for Applications (green for Data). The Galaxy Daemon won’t start. The log points to a problem mounting galaxyTools and indeed when I SSH in, /mnt/galaxyTools is absent. The log errors are: > > “Cannot retrieve reference to volume ‘None’; setting volume id to None. Error: EC2ResponseError: …’.0fb <… lots of characters> … c3aa9 > > And > > Error mounting file system ‘/mnt/galaxyTools’ from ‘/dev/sdg3’, running command ‘/bin/mount /dev/sdg3 /mnt/galaxyTools’ returned code ‘32’ and following stderr” ‘mount: you must specify the filesystem type ‘ > > > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan-Kettering Cancer Center may be privileged, confidential, > and protected from disclosure under applicable law. If the reader of > this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, > you are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this message > and deleting this message, any attachments, and all copies and backups > from your computer. >

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cloudman/galaxy on EC2 - snapshot not found
by Jorrit Boekel 14 Feb '12

14 Feb '12

Dear list, I am trying to deploy Galaxy as an environment for proteomics tools in amazon's EC2 cloud, probably/preferably via Cloudman. I have used both the biocloudcentral portal and a manual approach to set up cloudman/galaxy, but run into the same error message which seems to start with a problem with a snapshot that does not exist: * 15:16:05 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data' does not exist (yet?) * 15:16:26 - Error creating volume: EC2ResponseError: 400 Bad Request |InvalidSnapshot.NotFound|The snapshot 'snap-b28be9d5' does not exist.---some long identifier--- * 15:16:26 - Error adding filesystem service 'Filesystem-galaxyTools': 'NoneType' object has no attribute 'id' * 15:16:26 - STATUS CHECK: File system named 'galaxyTools' is not mounted. Error code 0 * 15:16:37 - Error mounting file system '/mnt/galaxyData' from '/dev/xvdg2', running command '/bin/mount /dev/xvdg2 /mnt/galaxyData' returned code '32' and following stderr: 'mount: you must specify the filesystem type ' My instance type is t1.micro (testing on AWS free tier), but I've tried m1.large, and that didn't help. I noted that the snapshot ID is always the same. Since the AMI is from March 2011 (at least the one I select manually), I assume that I have something wrong in my settings or that Amazon has changed something somewhere. cheers, Jorrit Boekel

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Error executing tool: 'hg19'
by Joachim Jacob 14 Feb '12

14 Feb '12

Hi, After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work. They all send this error message: Error executing tool: 'hg19' This bug has been reported before, but I was wondering if somebody suggest a fix for this? Thanks! Joachim.

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Running workflows on mulitple paired-end data sets
by Anthonius deBoer 14 Feb '12

14 Feb '12

Hi, Is there an intelligent way to run a workflow that starts with more than one pair of paired-end data sets in a workflow? I can run multiple workflows when there is a SINGLE input file, but in the case of many paired end workflows, you need to provide two paired samples and just adding another input workflow step does not work, since you can only select a single file in the second input workflow set. I realize that there is an issue with the cycling through the datasets since they need to be paired-up and it would be very easy to mess this up if you allow two (or more) input data sets, but since paired end data is going to be very common, I would assume a special paired end input workflow step that is intelligent and can pair up the input datasets before handing them off to the workflow would be very useful. I can think of workarounds ofcourse, such as creating an interlaced file containing both pairs and then just de-interlacing them in the workflow, but that is kludgy and will result in a lot of data duplication for no reason... I have to run 88 samples which will soon grow to over 200 samples, so running each step manually is not really an option and I would hate to have to program the workflow steps myself... Any ideas? Thanks Thon

2 1

history box odd behaviour
by Bossers, Alex 14 Feb '12

14 Feb '12

Hi All, Since some of the last updates (I guess, since I didn't notice it before) I notice some odd behaviour of the history box when for instance doing BLAST searches on our local galaxy_central (latest version). When I run blastx as output xml it starts running fine (yellow box). I can start new xml processors which are put in queue. All fine. When I press the eye icon on the running blast history box it drops an error in the mid panel that the xml is not there yet (XML-parse error). But than the box changes to green while the blast is still running in the background (checked with htop). The subsequent parsers remain in queue as well. Shouldn't the box remain yellow while processing? Or is something wrong with our datatype configurations...although I cannot remember we have changed anything in there. Thanks Alex

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2012 Galaxy Community Conference (GCC2012): Now Accepting Abstracts
by Dave Clements 13 Feb '12

13 Feb '12

Hello all, Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012) <http://wiki.g2.bx.psu.edu/Events/GCC2012>. Submissions on any topics of interest to the Galaxy community are encouraged. Areas of interest include, but are not limited to: - Best practices for local Galaxy installation and management - Integrating tools and/or data sources into the Galaxy framework - Deploying galaxy on different infrastructures - Compelling or novel uses of Galaxy for biomedical analysis See the GCC2011 program <http://wiki.g2.bx.psu.edu/Events/GCC2011> for an idea of the breadth of topics that can be covered. Oral presentations will be approximately 15-20 minutes long, including time for question and answer. There will also be an opportunity for lightning talks, which will be solicited at the meeting. The submission deadline is April 16. See the GCC2012 Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for more details and how to submit. GCC2012 <http://wiki.g2.bx.psu.edu/Events/GCC2012> will be held, July 25-27 in Chicago, Illinois, United States. The main meeting will run for two full days <http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>, and be preceded by a full day of training workshops<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>. If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, or a data and analysis archival specialist, then GCC2012 is relevant to you. Registration will open in March. GCC2012 is hosted by the University of Illinois at Chicago <http://uic.edu/>, the University of Illinois at Urbana-Champaign <http://illinois.edu/>, and the Computation Institute <http://www.ci.anl.gov/>. Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/Events/GCC2012/Abstracts Thanks, Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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