- galaxy-dev - lists.galaxyproject.org

missing file? (hapmapmart.xml)
by Erick Antezana 18 Nov '10

18 Nov '10

Hi, I just updated my local instance and it seems that the hapmapmart.xml is missing in the repository? galaxy.tools ERROR 2010-11-18 15:55:48,570 error reading tool from path: data_source/hapmapmart.xml Traceback (most recent call last): File "/tools/shared/bioinfo/app/galaxy/dev/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/tools/shared/bioinfo/app/galaxy/dev/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/tools/shared/bioinfo/app/galaxy/dev/lib/galaxy/util/__init__.py", line 102, in parse_xml tree = ElementTree.parse(fname) File "/tools/shared/bioinfo/app/galaxy/dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/tools/shared/bioinfo/app/galaxy/dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/hapmapmart.xml' thanks, Erick

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Problem with Mako and Beaker egg...
by Marc Bras 17 Nov '10

17 Nov '10

Hi, I'm trying to install Galaxy in a production environment. Since I set Postgres DataBase, I've got this warning when I launch any tool: /WARNING:galaxy.eggs:Warning: Beaker (a dependant egg of Mako) cannot be fetched/ And this warning is print in STDERR... so the tool failed... I don't know why it can't fetch Beaker egg... I aldready try to remove : - $GALAXY_ROOT/eggs/Beaker-1.4-py2.5.egg - $GALAXY_ROOT/eggs/Mako-0.2.5-py2.4.egg - $GALAXY_ROOT/eggs/Mako-0.2.5-py2.5.egg but I've got still the problem. I'm open to any solution !! Many thanks for your help, Marc

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galaxy behind proxy/apache2
by Bossers, Alex 17 Nov '10

17 Nov '10

Hello all, I am trying to do the production server setup of galaxy and was finally succesfull in using mysql instead of sqlight. I am facing difficulties in configuring the proxy/apache part though. I followed the wiki but no luck. I do not have any other sites on that machine but I was hoping to either: use www.domain.nl/galaxy<http://www.domain.nl/galaxy> or www.domain.nl:8080<http://www.domain.nl:8080/> to point to the galaxy using apache and proxy.... that would leave the possibility to have www.domain.nl<http://www.domain.nl/> and/or www.domain.nl/other_sites<http://www.domain.nl/other_sites> to still be used. My www is at default /var/www Galaxy is in /opt/galaxy mod-rewrite is installed and enabled even as the proxy parts made the suggested modifictions to universe_wsgi.ini (unsure on the server=0.0.0.0 or 127.0.0.1 part and the part dealing with the setting of the static part... should that be True or False. I would say False. Just to be sure: galaxy must be started using its own galaxy system user right? Apache2 is working fine (on ubuntu maverick server) and the www.domain.nl<http://www.domain.nl/> site incl PHP is working. Also www.domain.nl/phpmyadmin<http://www.domain.nl/phpmyadmin> is fully functional.... I'm puzzled... Any help/direction is appreciated. Or a working example of the universe_wsgi.ini and other config files would be very helpful! Alex

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Send file to 3rd party site
by Chris Zaleski 17 Nov '10

17 Nov '10

Greetings, I have a Galaxy tool we use to send files to another website - I used "data_destination/epigraph.xml" as a template. In this case, the other website is our own web-based database system. Everything is on our own internal network. This was working fine until I recently did a major Galaxy update. We were running a large production pipeline, and intentionally did not upgrade Galaxy for over a year. The problem seems to be when the outside system uses the "DATA_URL" parameter to get the file from Galaxy. Instead of getting the data file, Galaxy returns a HTML file (which seems to be the index page of Galaxy itself). I did a couple tests, and realized that this behavior changes depending on the client using the "DATA_URL". It works in a browser, but fails in other cases: 1) If I take the "DATA_URL", and paste it directly into a browser address bar (Firefox), it works properly. I get the data file I'm supposed to get. 2) In the case of my outside database system, it uses PHP's "copy" function. What gets copied is the incorrect HTML file. 3) I tried using "wget" with the "DATA_URL", and it also gets the same incorrect HTML file. You can see in the wget output that it receives a redirect - the redirected URL turns out to the be galaxy homepage. So maybe PHP's copy function and wget are both getting redirected, but Firefox is not...? I'll attach the wget output, as well as the incorrect HTML file I'm getting from Galaxy. Any help is greatly appreciated. Thanks Chris Zaleski

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Upload to Galaxy via FTP
by Nate Coraor 17 Nov '10

17 Nov '10

Reposted to the Development list for the benefit of those not on the User list. Hello, With the continued advancement of sequencing technology, we've seen the size of files uploaded to Galaxy grow quite large. Although our current file upload methods have worked fine for years, they are not well suited for the extremely large files in common use today. Uploading directly from the browser can be unreliable and browsers don't provide feedback on upload progress and state like they do for downloads. Because of this, we have implemented file uploads to Galaxy via FTP. FTP will allow you to monitor as mentioned above, as well as resume interrupted transfers. To get started using FTP, you'll need to have registered a regular Galaxy account on our public server at: http://main.g2.bx.psu.edu/ Once registered, you can initiate an FTP connection in your preferred FTP client to the same host (main.g2.bx.psu.edu) using your registered email address and password for the login details. Files uploaded to this server won't automatically be imported to Galaxy - rather, you will be presented with a list of the contents of your FTP directory on the standard "Upload File" tool interface. Files not imported within 3 days will be cleaned up from the FTP site. We hope that this service solves a crucial problem in data transfer speed and reliability. Please report any problems or suggestions with the service to us at: galaxy-bugs(a)bx.psu.edu Please note that it may not always be practical to use the public Galaxy servers. If you're routinely working with very large data and having to wait for it to upload, a local Galaxy server could be a more practical solution. Instructions on installing your own server can be found at: http://getgalaxy.org/ http://usegalaxy.org/production In addition, with the recent announcement of Amazon's parallel upload capability for the Simple Storage Service (S3), we are investigating incorporating easy access to S3 buckets for Galaxy instances on the Amazon Elastic Compute Cloud (EC2). But you don't need to wait for the pretty interface, you can already access contents of S3 buckets by pasting links to their contents in the "URL/Text:" field of the "Upload File" tool. For an example of how to do this, see the "Watch how the complete analysis can be performed on the Amazon Cloud" screencast at: http://usegalaxy.org/heteroplasmy Thanks, --nate Galaxy Team

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rpy for Galaxy?
by David Hoover 17 Nov '10

17 Nov '10

I am having great difficulty installing rpy (v1.0.3) for our local Galaxy installation. Is rpy actually supported for Galaxy? Should I even bother trying to install rpy? David Hoover Helix Systems Staff http://helix.nih.gov

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iframe target links with external projector
by Brad Chapman 17 Nov '10

17 Nov '10

Hi all; I'm giving a live demo of Galaxy in a few hours and was prepping with my laptop attached to an external projector. When connected to the projector, the target links in the sidebar load in the full window instead of targeting the galaxy_main iframe. This gets rid of the nice 3 panel layout. On the same machine the target links works as expected if my laptop is not connected to the external projector. Has anyone here seen the same issue when giving a Galaxy demo? Any configuration tips or tricks for Firefox (3.6) that will help? Thanks much, Brad

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Feature Update: Expanded Reference Genomes for NGS Tools
by Jennifer Jackson 16 Nov '10

16 Nov '10

Feature Update: Expanded Reference Genomes for NGS Tools Expanded genome data is now available on Galaxy's main server http://usegalaxy.org. The expanded genome data are organized into the following categories: Full = All chromosomes (or scaffolds/contigs) released as part of the full build from the data source. Many will also include the latest Mitochondrial chromosome, if available. Full is the default genome build type for all reference genomes and what was previously available. Canonical = All chromosomes released that represent the core chromosomes (including mitochondrial) for that species and build. Canonical will not include chromosomes with names that include: chrUn, chrN_random, chrN_hap_XX (haplotype), and similar. Coming soon will also be the reference genome variants Male and Female. Many genomes will default to Male (identical to Canonical). Female will be the Canonical minus a chrY chromosome. The NGS Tools with expanded genome data available: Bowtie and BWA. Please note that previously used/saved settings will default to "Full". Other NGS Tools are planned to have expanded reference genome data available in the future as appropriate. Reference genomes part of the expanded dataset include: galGal3 hg18 hg19 mm8 mm9 panTro2 rn4 taeGut1 tetNig1 tetNig2 Thanks for using Galaxy! Galaxy team November 16, 2010

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Galaxy/Python and Bioinformatics Engineers positions at the J.Craig Venter Institute
by Krampis, Konstantinos 16 Nov '10

16 Nov '10

Hi all, We have a few open Bioinformatics/Software Engineers positions at the J.Craig Venter Institute, one of which involves largely developing further the Galaxy platform for use in-house (writing additional Galaxy wrappers for internal pipelines / tools, integrating Galaxy with existing cluster systems, SGE etc.) Besides working with Galaxy, these positions involve quite a broad range of software development opportunities (languages ranging from Perl to Java), while at the same time they offer great learning opportunities for working with next- generation sequencing datasets, and learning fundamental techniques related to bioinformatic analysis of these types of data. Please pass the word, feel free to email me for additional information, or even go to the careers page to apply: https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlP… many thanks ! -- Konstantinos (Ntino) Krampis, Ph.D. Bioinformatics Engineer J.Craig Venter Institute Cell. 540-200-8277 http://twitter.com/agbiotec

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Running job status not working
by Chris Cole 16 Nov '10

16 Nov '10

Hi, Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get: galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks, Chris

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