September 2013 - galaxy-user - lists.galaxyproject.org

main galaxy server is down?
by Boaz Shaanan 30 Sep '13

30 Sep '13

Hi, Is the main galaxy server down? Or very sloooow? I have a Lastz job (not too demanding and one that has been run several times before) waiting for a long time already. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

3 2

October Galaxy Update Newsletter is out
by Dave Clements 30 Sep '13

30 Sep '13

Hello all, The October 2013 Galaxy Update is out<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10> : *Highlights:* - A record *six new public servers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Public_Servers> * - 44 new papers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Papers> - Open Positions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Who.27s_Hiring> at nine different organizations - Upcoming Events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Events>, lots of them in Australia<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Australia.21> plus 3 other continents<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#All_Those_Other_Contine…>. - Online materials from past events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Online_Materials_from_P…>, including all GCC2013 videos on Vimeo <http://bit.ly/gcc2013vimeo> and course materials for the 2013 UC Davis Bioinformatics Short Course<http://bit.ly/16rAUkf>. The UC Davis course featured 5 great days of lecture and hands-on exercises. - More Tool Shed contributions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Tool_Shed_Contributions> than you can shake a stick at. If you have anything you would like to see in the next *Galaxy Update<http://wiki.galaxyproject.org/GalaxyUpdates> *, please let us know. Dave Clements and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Built-in Editor
by Isaac Knoflicek 30 Sep '13

30 Sep '13

Is it possible to use ACE or some other type of in line editor to modify files in Galaxy? Like if we had a tool that accepted as a parameter a file written in a homegrown modeling language, is there any way to update that file without downloading and re-uploading? Has anyone seen or done anything like this? Thanks, Isaac Knoflicek IT Manager - Laboratory of Genetics University of Wisconsin - Madison

2 1

How to become admin on Galaxy Cloudman
by Yan He 30 Sep '13

30 Sep '13

Hi all, I just established Galaxy Cloudman on Amazon EC2. I would like to add some tools in tool shed to to it. However, I need to be the admin to do this. Once I got into the galaxy cloudman, I had to register a new account and then log in. The admin interface (described in tool shed wiki) didn't appear at all. How could I log in as admin on Galaxy Cloudman? This may be a very simple question, but it bothers me two days. Looking forward to your replies! Best wishes, Yan

2 2

SNP calling problems
by garzetti 27 Sep '13

27 Sep '13

Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources but with no success. I am sorry if this topic has been already discussed! So, I am analyzing MiSeq data on the main Galaxy. I have Fastq files from 4 paired-end samples. After having checked the quality with FastQC and groomed them, I have performed a BWA mapping, filtered the results and converted the SAM to BAM files (for each sample separately). I have then called SNPs with Freebayes and SAMtools, encountering problems in both cases. 1) SAMtools: if I run the Generate pileup tool, then the Filter pileup doesn't recognize any valid format in the files I have in my History and I cannot go on with the analysis. Why is that? What can I do? 2) I have performed variant calling with Freebayes on single BAM files and on one merged BAM files from all my four BWA mapping files. In all cases, the last column is "unknown", while it should be the name of my sample. This is not a big deal for the single vcf files, but from the merged BAM file, I cannot discriminate from which sample the SNPs were detected. I think there is a problem in the BAM files which are not properly indexed. Also Freebayes needs an RG tag. Is there a tool in Galaxy I can use to index BAM files, adding the RG tag? I hope someone can help me! Thank you very much! Debora -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: garzetti(a)mvp.uni-muenchen.de Phone: +49 (0)89 2180 72915

2 1

database of known ChIP-seq peaks
by Bogdan Tanasa 27 Sep '13

27 Sep '13

Dear all, please could you recommend any resource/collection/database of known ChIP-seq tracks that also include a significance analysis tool ? thanks, Bogdan

2 1

cleanup_datasets.py with postgresql 8.1
by Malcolm Tobias 27 Sep '13

27 Sep '13

All, My understanding is that the cleanup_datasets.py under scripts/cleanup_datasets should be compatible with 'older' versions of postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the scripts, it fails to clean any data sets. From the logs, I'm noticing messages like: database_connection contains an unknown SQLAlchemy database dialect: postgresql In my universe_wsgi.ini I've defined the database_connection as: database_connection = postgresql://galaxy:********@localhost:5432/galaxydb and am confident it's working as Galaxy works fine, other than this problem with deleting older datasets. The pgcleanup.py script isn't an option, as it requires postgresql >=9.1. I noticed yet another version of cleanup_datasets.py under cron which looks like it might be compatible with postgres, but am leary of trying it as I'm not sure what it means by "1: database directory to clean". I'm not sure what directory to point this to, nor am I confident that just deleting data from the directory is the safest thing. Any suggestions on how to proceed? Thanks! Malcolm -- Malcolm Tobias 314.362.1594

2 1

generating pileup with max depth greater than 8000?
by Lauren Oldfield 26 Sep '13

26 Sep '13

My question: How can I generate a pileup with an output of more than 8000 hits per base? I was generating pileups using the SAM tools --> Generate pileup and do not see an option to change the settings for output. In mpileup there is a variable that looks correct, -D (Output per-sample read depth) , but I cannot figure out how to adjust it. I checked the box, Output per-sample read depth, under the advanced settings but the log file generated still says the max depth was 8000. The pileup files I generated look great but I would like to know what the true read depth is at the 8000 hit plateaus. Any help appreciated. I'm a little out of my depth here. -- Lauren M. Oldfield Hatfull Laboratory Dept. of Biological Sciences University of Pittsburgh 376 Crawford Hall 4249 Fifth Ave Pittsburgh, PA 15260 412-624-6976

3 2

Trying to visualize 2 bam files from Galaxy
by Ben Gift 26 Sep '13

26 Sep '13

I'm trying to start a visualizer with two different files to show a person where the variants are. Can I start IGV or something like it with multiple files? I read the docs and didn't find anything about it. I also asked here http://www.biostars.org/p/82032/

3 2

Variant Annotation in GATK tools
by Yan He 26 Sep '13

26 Sep '13

Hi all, I am analyzing some targeted resequencing data. I was trying to use Variant Annotation tool under GATK after got .VCF file. But some error as following returned. Would you please help me to figure out what happened? Or this tool can only be used for some model organisms? Thanks a lot! "An error occurred with this dataset: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Wed Sep 25 03:59:41 EDT 2013] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/space/g2main/tmp-gatk-4SDjhY/gatk_input.fasta OUTPUT=/space/g2main/tmp-gatk-4SDjhY/dict5123971853428830433.tmp" Yan

2 1