January 2014 - galaxy-user - lists.galaxyproject.org

Creating a Trackster visualisation from a reference in your history
by graham etherington (TSL) 23 Jan '14

23 Jan '14

Hi, I’m struggling to figure out how to visualise a SAM file in Trackster as a normal user (i.e. without admin privileges). I’ve tried both my local install and use galaxy.org. This is what I’ve done on usegalaxy.org: Uploaded paired-end fastq sequences and a reference fasta file. Mapped with BWA. Clicked on SAM output – Visualize > Trackster Chose 'View in new visualisation’, then ‘Add a Custom Build’. In the ‘Add a Custom Build’ I give my build the name ‘solanum_reference’ and the key ‘solanum_reference_1’. I select the fasta mapping reference from my history under the ‘FASTA’ tab and under the Len File entry I upload a .len file (tab-delimited) called ‘solanum_reference_1.len’. I navigate back to my SAM history item, associate the Database/Build with my new build (via the Edit attributes icon) and then again Visualize > Trackster > View in New Visualization. I name the Browser, select my ‘solanum_reference’ as the 'Reference genome build' and hit ‘Create’. The view changes to the Trackster Browser and at the top I reads: "Preparing data, This can take a while for a large dataset…..etc., etc. " After a few minutes, this changes too: “Cannot display dataset due to an error.” If I click on ‘View error’ I get: Couldn't open /galaxy/data/chrom/solanum_reference_1.len , No such file or directory Is it possible to create a custom build and use it to view a SAM file without adding the .len and .2bit files in to the Galaxy file system as an administrator? If so, what am I doing wrong? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

3 2

Question in converting gtf file for p_id
by Yanxiang Shi 22 Jan '14

22 Jan '14

Hi all, I've been trying to use the cufflinks-cuffmerge-cuffdiff flow to analyze my RNAseq data. However, cuffmerge lost my p_id. My p_id was originally from changing the protein_id to p_id by myself in the gtf file. The current p_id showed up in the same attributes column as gene_id in the gtf file. Does anyone know how to make it reachable by cuff? I'm using galaxy public platform. Apparently in the history people say solving the problem by writing an extra code. But I cannot find anywhere to input codes in galaxy. Do I have to run everything on my own computer? Thanks a lot!!!!! Nancy

2 3

problem uploading files
by Emmanuelle Lerat 21 Jan '14

21 Jan '14

Hello everyone I am trying to upload files on galaxy main since yesterday and I can't get it work. The files I want to upload are RNAseq fastq files from ENCODE (about 8 Go in size). So I first tried to use the http address of the files. The job is running forever but without finishing and without error message. I also tried using FTP but in that case, I could not connect to the main.g2.bx.psu.edu server (I get the message "ECONNREFUSED - Connection refused by server"). I am using my email address as login (the same as for galaxy login) and the same password. Do I do something wrong or is there a global problem? Thank you in advance for your help. Sincerely Emmanuelle -- Dr. Emmanuelle LERAT, CR1 CNRS, HDR Laboratoire Biometrie et Biologie Evolutive Universite Claude Bernard - Lyon 1 UMR-CNRS 5558 - Bat. Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne cedex France Phone: 33+ 4.72.43.29.18 Fax: 33+ 4.72.43.13.88 http://lbbe.univ-lyon1.fr/-Lerat-Emmanuelle-.html

2 1

usegalaxy.org is down?
by Leontovich, Alexey A., Ph.D. 20 Jan '14

20 Jan '14

Hello, It seems that usegalaxy.org is down. Is it? Thank you. Alexey Leontovich

2 1

error:ordinary output of macs in stderr
by 韩宏庆 20 Jan '14

20 Jan '14

Hello, galaxy users and developers, I wrote a perl script conducting saturation analysis which called macs several times.The tool's output was right but ,errorAn error occurred with this dataset:INFO @ Sat, 18 Jan 2014 21:46:33: # ARGUMENTS LIST: # name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output # format = BED # ChIP-seq file = 0.test.bed # control file = 0.control.bed # effective genome size = 2.70e+09 # tag size = 2 Tool execution generated the following error message: INFO @ Sat, 18 Jan 2014 21:46:33: # ARGUMENTS LIST: # name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output # format = BED # ChIP-seq file = 0.test.bed # control file = 0.control.bed # effective genome size = 2.70e+09 # tag size = 28 # band width = 300 # model fold = 16 # pvalue cutoff = 1.00e-05 # Ranges for calculating regional lambda are : peak_region,1000,5000,10000 INFO @ Sat, 18 Jan 2014 21:46:33: #1 read tag files... INFO @ Sat, 18 Jan 2014 21:46:33: #1 read treatment tags... INFO @ Sat, 18 Jan 2014 21:46:37: #1.2 read input tags... INFO @ Sat, 18 Jan 2014 21:46:39: #1 Background Redundant rate: 0.04 INFO @ Sat, 18 Jan 2014 21:46:39: #1 finished! INFO @ Sat, 18 Jan 2014 21:46:39: #2 Build Peak Model... INFO @ Sat, 18 Jan 2014 21:46:47: #2 number of paired peaks: 11875 INFO @ Sat, 18 Jan 2014 21:46:47: #2 finished! INFO @ Sat, 18 Jan 2014 21:46:47: #2.2 Generate R script for model : /usr/local/galaxy-dist/database/job_working_directory/000/0.output_model.r INFO @ Sat, 18 Jan 2014 21:46:47: #3 Call peaks... INFO @ Sat, 18 Jan 2014 21:46:47: #3 shift treatment data INFO @ Sat, 18 Jan 2014 21:46:47: #3 merge +/- strand of treatment data INFO @ Sat, 18 Jan 2014 21:46:47: #3 call peak candidates INFO @ Sat, 18 Jan 2014 21:46:48: #3 shift control data INFO @ Sat, 18 Jan 2014 21:46:48: #3 merge +/- strand of control data INFO @ Sat, 18 Jan 2014 21:46:48: #3 call negative peak candidates INFO @ Sat, 18 Jan 2014 21:46:48: #3 use control data to filter peak candidates... INFO @ Sat, 18 Jan 2014 21:46:48: #3 Finally, 2003 peaks are called! INFO @ Sat, 18 Jan 2014 21:46:48: #3 find negative peaks by reversing treat and control INFO @ Sat, 18 Jan 2014 21:46:49: #3 Finally, 120 peaks are called! INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.xls INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output bed file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.bed INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file for negative peaks... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_negative_peaks.xls INFO @ Sat, 18 Jan 2014 21:46:49: #5 Done! Check the output files! Just ordinary macs output, we see it in galaxy-macs report. The only problem is that they're in stderr. With this error I cannot do other works with the output of this tool.How can I deal with it?Thanks! -Han --------------------------------

2 1

re
by Larry 19 Jan '14

19 Jan '14

Hi I have a question about the use of BedTools in Galaxy. I am trying to obtain a graph or table of the number of RNA reads mapped to different locations on my custom genome. When I try running "Create a Bedgraph of Genome Coverage" it requires selection of the "Genome Build" from a dropdown list. Is it possible for the program to utilize a custom genome not in this list? Larry Simpson UCLA

2 1

GATK2 Galaxy wrapper available, testing and help needed
by Björn Grüning 18 Jan '14

18 Jan '14

Hi all, over the last month we developed a new version of GATK2 wrappers and are now seeking for testers, users and overall feedback. We are currently targeting GATK 2.8. One of the big issues with GATK2 is the new licence. Because of that we can't install GATK2 with the wrappers, but we hope we have done it as easy as possible to plugin your local installed version. Furthermore, we made it easy to disable the 'call home feature' of GATK2 (if you have a GATK keyfile). Read more about it: https://github.com/bgruening/galaxytools/blob/master/gatk2/readme.rst The code is stored here: https://github.com/bgruening/galaxytools/tree/master/gatk2 The ToolShed wrappers can be found here: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2 I would like to thank Jim Johnson, Nicola Soranzo, Dan Blankenberg and the Galaxy Team. If you like the wrappers you know what to do during the next GCC! If you have feedback or patches please let us know. Thanks, Bjoern

1 0

Galaxy Australasia Workshop (GAW 2014), 24-25 March, Melbourne
by Dave Clements 17 Jan '14

17 Jan '14

Hello all, *We are pleased to announce the 1st Galaxy Australasia Workshop 2014 (GAW 2014) <https://wiki.galaxyproject.org/Events/GAW2014> will be held in Melbourne, Australia on 24 and 25th March 2014.* The Galaxy Australasia Workshop<https://wiki.galaxyproject.org/Events/GAW2014> is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch <http://wp.csiro.au/css/> in Melbourne. GAW 2014 will also include poster session, keynote speakers. *You should attend to:* - Present your work! - Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets. - Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them. - Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction. - Learn - how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics) - how to share, publish, and reuse your analyses with Galaxy - how to perform and enable your users to perform common, yet complex, analyses using Galaxy - when and how to use Galaxy on the Cloud *Topics will potentially include:* - Image analysis and processing using Galaxy. - RNAseq/ChIPseq/Variant Calling/RNA Quality Control. - Galaxy on the Research Cloud. - CSIRO galaxy service - partnership between science and IT. - Identifying proteins from mass spec data with Galaxy. *Call For Abstracts* Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit a brief one-page abstract and brief one-paragraph bio to the GAW2014 Organisers <gaw2014-org(a)groups.galaxyproject.org> *by February 15th, 2014.* Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance. Submissions should clearly state whether they are for: poster or oral presentation. Looking forward to seeing you all in Melbourne! GAW 2014 Organising Committee<https://wiki.galaxyproject.org/Events/GAW2014#Organising_Committee> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Trying to "unshare" a history in order to delete
by zod 16 Jan '14

16 Jan '14

Hi, I shared a history with another user and I am now trying to delete said history. When I go to delete it I am told to unshare it first. I found one message in the [dev] list which says to click the "shared" link when viewing Saved Histories and choose "unshare". When I do this nothing happens. When I had the other user (who has a button which says "unshare" for this history) click "unshare" that user is told they can't unshare it. How to go about this? Jen, maybe you can add deleting shared histories to your deleting/disk space video? Thanks, David FHCRC

2 3

all FPKMs are 0 in the tmap files produced by cuffcompare
by Yang Bi 14 Jan '14

14 Jan '14

Dear all: I am new to Galaxy and I followed online tutorials/tips to analyze my RNA seq data for alternative splicing. I used "tophat for illumina" to align my sequencing data after QC/filtering. Other than setting min intron to 20, I used the default settings. Then I feed the accepted hit files to cufflink. I set Min isoform fraction to 0, use annotation (tair10 gff3) as guide and choose yes for perform bias correction (locally cached tair10). I merged the assembled transcripts with cuffmerge and use cuffcompare to compare the resultant merged assembled transcript to the reference annotation file tair10 gff3. I choose yes for "use sequence data" and locally cached tair10 as the "reference list". I get this for the transcript accuracy analysis: # Cuffcompare v2.1.1 | Command line was: #cuffcompare -o cc_output -r /galaxy-repl/main/files/007/386/dataset_7386886.dat -s /galaxy/data/Arabidopsis_thaliana_TAIR10/sam_index/Arabidopsis_thaliana_TAIR10.fa ./input1 # #= Summary for dataset: ./input1 : # Query mRNAs : 72778 in 51779 loci (57559 multi-exon transcripts) # (12679 multi-transcript loci, ~1.4 transcripts per locus) # Reference mRNAs : 42163 in 33350 loci (30127 multi-exon) # Corresponding super-loci: 33140 #--------------------| Sn | Sp | fSn | fSp Base level: 100.0 62.7 - - Exon level: 104.6 59.5 100.0 60.5 Intron level: 100.0 55.5 100.0 56.5 Intron chain level: 98.3 51.5 100.0 60.3 Transcript level: 98.7 57.2 94.8 54.9 Locus level: 99.4 64.0 100.0 64.1 Matching intron chains: 29618 Matching loci: 33147 Missed exons: 1/169820 ( 0.0%) Novel exons: 128021/298149 ( 42.9%) Missed introns: 0/127896 ( 0.0%) Novel introns: 102614/230568 ( 44.5%) Missed loci: 1/33350 ( 0.0%) Novel loci: 2962/51779 ( 5.7%) Total union super-loci across all input datasets: 51779 For the tmap file, all my FPKMs are 0: ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len AT1G01010 AT1G01010.1 = AT1G01010 TCONS_00000001 0 0.000000 0.000000 0.000000 0.000000 1688 TCONS_00000001 1688 AT1G01040 AT1G01040.1 = AT1G01040 TCONS_00000002 0 0.000000 0.000000 0.000000 0.000000 6251 TCONS_00000002 6251 AT1G01040 AT1G01040.2 = AT1G01040 TCONS_00000003 0 0.000000 0.000000 0.000000 0.000000 5877 TCONS_00000002 5877 AT1G01046 AT1G01046.1 = AT1G01046 TCONS_00000004 0 0.000000 0.000000 0.000000 0.000000 207 TCONS_00000004 207 AT1G01073 AT1G01073.1 = AT1G01073 TCONS_00000005 0 0.000000 0.000000 0.000000 0.000000 111 TCONS_00000005 111 AT1G01110 AT1G01110.2 = AT1G01110 TCONS_00000006 0 0.000000 0.000000 0.000000 0.000000 1782 TCONS_00000006 1782 AT1G01110 AT1G01110.1 = AT1G01110 TCONS_00000007 0 0.000000 0.000000 0.000000 0.000000 1439 TCONS_00000006 1439 AT1G01115 AT1G01115.1 = AT1G01115 TCONS_00000008 0 0.000000 0.000000 0.000000 0.000000 117 TCONS_00000008 117 AT1G01160 AT1G01160.1 = AT1G01160 TCONS_00000009 0 0.000000 0.000000 0.000000 0.000000 1045 TCONS_00000010 1045 AT1G01160 AT1G01160.2 = AT1G01160 TCONS_00000010 0 0.000000 0.000000 0.000000 0.000000 1129 TCONS_00000010 1129 AT1G01180 AT1G01180.1 = AT1G01180 TCONS_00000011 0 0.000000 0.000000 0.000000 0.000000 1176 TCONS_00000011 1176 AT1G01210 AT1G01210.1 = AT1G01210 TCONS_00000012 0 0.000000 0.000000 0.000000 0.000000 616 TCONS_00000012 616 AT1G01220 AT1G01220.1 = AT1G01220 TCONS_00000013 0 0.000000 0.000000 0.000000 0.000000 3532 TCONS_00000013 3532 The FPKMs were normal in the assembled trancripts produced by cufflink. Please enlighten me on the possible mistakes that i have made. I really appreciate your help. Best Yang

2 5