November 2012 - galaxy-user - lists.galaxyproject.org

Find out sense and antisense sequences
by Zhiqiang Shu 27 Nov '12

27 Nov '12

Hi, Galaxy users! I have a question on how to find out sense and antisense sequence. I've got RNA seq data in the fastq format. The sequences inside are partially complementary to each other (complementary is 10nt, while entire is about 30nt). How can I separate these sequences into two groups: sense and antisense (one thing I know is for the sense sequence the 10th nucleotide is always "A")? Thanks a lot! Best, Zhiqiang

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BWA mapping with index file from history
by shamsher jagat 26 Nov '12

26 Nov '12

I have a Hi-seq Single end data and want to align it to a viral genome and have fasta file of viral genome. I have created index files out side Galaxy (I believe I cannot create index file with in Galaxy). The question which I have is: There are various index files (v.fasta.amb; v.fasta.pac; v.fasta.rbwt; v.fasta.rpac; v.fasta.sa) should I be using all the these files as zip file for index file or one (which one?). Thanks Kanwar

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Why is 'Filter pileup' not recegnising my 'Generate pileup' file?
by Jacqui Stockley 26 Nov '12

26 Nov '12

Hi, I was wondering if you could help me with a problem I have been having recently. I have carried out a number of NGS analyses using SAM Tools where I have generated pileup and then filtered this file using the filter pileup tool. However, recently when I have tried to do this the filter pileup is not recognising a compatible dataset in the history (ie it is not recognising the generate pileup file). I have always done the same so I can't understand what I might have done wrong. I have gone into old datasets and tried to filter pileups from previous histories and they also do not recognise the generate pileup file despite the fact they have previously! Is there something I am doing majorly wrong or should I be using another function? Many thanks for any help or advice! Jacqui

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New Galaxy CloudMan Release
by Enis Afgan 25 Nov '12

25 Nov '12

*We just released an update to CloudMan.* CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration. *This update brings a large number of updates and new features, the most prominent ones being:* - Support for Eucalyptus cloud middleware. Thanks to Alex Richter. Also, CloudMan can now run on the HPcloud in basic mode (note that there is no public image available on the HPcloud at the moment and one would thus need to be built by you). - Added a new file system management interface on the CloudMan Admin page, allowing control and providing insight into each available file system - Added quite a few new user data options. See the UserData page<http://wiki.g2.bx.psu.edu/CloudMan/UserData>for details. Thanks to John Chilton. - Galaxy can now be run in multi-process mode. Thanks to John Chilton. Added Galaxy Reports app as a CloudMan service. Thanks to John Chilton. - Introduced a new format for cluster configuration persistence, allowing more flexibility in how services are maintained - Added a new file system service for instance's transient storage, allowing it to be used across the cluster over NFS. The file system is available at /mnt/transient_nfs just know that any data stored there* will not be preserved* after a cluster is terminated. - Support for Ubuntu 12.10 - Worker instances are now also SGE submit hosts This update comes as a result of 175 code changesets; for a complete list of changes, see the commit messages<https://bitbucket.org/galaxy/cloudman/changesets/tip/3a63b9a40331%3A35baec1> . Any new cluster will automatically start using this version of CloudMan. Existing clusters will be given an option to do an automatic update once the main interface page is refreshed. Let us know what you think, Enis

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help
by Dr. Mira A. Bisso 21 Nov '12

21 Nov '12

Hello; I am having the following problems with RNAseq using galaxy; we have installed the Galaxy local version on local server. 1. FastQC not running . gives an error and doesn't run on groomed or un-groomed FastQ file. The error message shows in the below pic. 2. No reference genomein the drop down list in TOPHAT for illumine tool and TOPHAt2. Any solution? Thank you Mira [image001] Mira Bosso, M.Sc, B.D.S Research associate Pancreatic Islet Biology and Transplantation Unit P.O.Box 1180, Dasman 15462, Kuwait Phone: +965 2224 2999 Ext.2803 Mob: +96599500197 Email: mira.bisso(a)dasmaninstitute.org<mailto:mira.bisso@dasmaninstitute.org>

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Curious-- what does "You are currently viewing a deleted history!" mean?
by Bob Harris 20 Nov '12

20 Nov '12

Howdy, A couple weeks ago I popped up main.g2.bx.psu.edu and, without logging in, submitted a small megablast job, then forgot about it. Today I remembered that job and went back to look at it. The results are there (hurray!) but I am confused by the notification that "You are currently viewing a deleted history!" What does this mean? My best guess is that this data has been marked for deletion but the disk space hasn't been reclaimed yet. Is that correct? If so, there must be a better way to say that to the user. I don't need these results after seeing them, but would a novice user understand this message means he/she needs to take some action to preserve their results? Just curious, Bob H

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Unmapped reads from tophat
by Kevin Y 20 Nov '12

20 Nov '12

Hello, Is there a way to get unmapped reads from tophat? The accepted hits bam output only contains mapped reads (confirmed with flagstat) Am I overlooking an option or tool? Thanks Kevin

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Local Install - Understanding Upload File Concept
by greg 16 Nov '12

16 Nov '12

I'm confused if files are uploaded through the Galaxy server or through Apache? I already set up the Apache proxy explained here: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy (Does that affect uploads?) My goal is to let users upload as large of files as possible through HTTP. So far I just tested and upload of a 140MB file and I got this error after a couple of minutes: 1: dsim-all-chromosome-r1.3.fasta.msg.updated.fasta 0 bytes An error occurred running this job:Traceback (most recent call last): File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in <module> __main__() File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 359, in __main__ registry.load_datat I see this information in the bug report: Traceback (most recent call last): File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in <module> __main__() File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 359, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 65, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/misc/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in parse_xml tree = ElementTree.parse(fname) File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line 859, in parse File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line 576, in parse IOError: [Errno 2] No such file or directory: '/scratch/galaxy/tmptzuSYJ' Traceback (most recent call last): File "./scripts/set_metadata.py", line 118, in <module> __main__() File "./scripts/set_metadata.py", line 68, in __main__ datatypes_registry.load_datatypes( root_dir=config_root, config=datatypes_config ) File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 65, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/misc/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in parse_xml tree = ElementTree.parse(fname) File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line 859, in parse File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line 576, in parse IOError: [Errno 2] No such file or directory: '/scratch/galaxy/tmptzuSYJ' Also here is what /scratch/galaxy looks like. It seems like the file it mentions does exist?? >ls -lh /scratch/galaxy/ total 134M -rw-r--r-- 1 galaxy scicomp 20K Nov 13 13:35 tmpfCaiGX -rw-r--r-- 1 galaxy scicomp 20K Nov 14 13:36 tmpM2Wclq -rw-r--r-- 1 galaxy scicomp 20K Nov 14 13:35 tmpsIyPur -rw-r--r-- 1 galaxy scicomp 20K Nov 16 08:48 tmptY5RaM -rw-r--r-- 1 galaxy scicomp 20K Nov 16 08:54 tmptzuSYJ -rw-r--r-- 1 galaxy scicomp 20K Nov 15 15:47 tmpu77PEK -rw------- 1 galaxy scicomp 286 Nov 16 08:58 tmpykoBIq -rw------- 1 galaxy scicomp 134M Nov 16 08:58 upload_file_data_G3eZEg Thanks, Greg

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Galaxy server configuration - what is [server:main]?
by greg 16 Nov '12

16 Nov '12

I see this setting at the top of universe_wsgi.ini: # Configuration of the internal HTTP server. [server:main] I'm confused what that's for. Do I need to change it? Thanks, Greg

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SNPeff on human genome
by David Sims 15 Nov '12

15 Nov '12

Hi, Is it possible to use SNPeff with genomes other than worm. This seems to be the only option on the main Galaxy server. Thanks, David

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