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

Upload files not working?
by Daniel Sher 22 Jan '13

22 Jan '13

Hello Galaxy team – the upload files tool does not seem to be working in the last few hours (small jobs in list but not running). Is there a problem with the server? Thanks Daniel -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office +972-4-8240731 Lab +972-4-8288961 email: dsher(a)univ.haifa.ac.il http://marsci.haifa.ac.il/mce

4 3

"spot" EC2 instances for Galaxy?
by Andrew Norman 18 Jan '13

18 Jan '13

Hi I'm wondering if anyone has had experience running Galaxy using the Amazon "spot" EC2 instances? These instances are charged based on a bid placed by the user, and only run when the bid exceeds exceeds the current spot price. In other words, you pay a significantly reduced rate for cloud capacity but it runs intermittently. This is OK for certain applications but I'm not sure how that will work for Galaxy. Specifically, I'm interested in using Galaxy for Tophat analysis of RNA seq datasets. Any insight that anyone has will be helpful. Thanks! Andy

2 1

Workflows
by Neil.Burdett＠csiro.au 18 Jan '13

18 Jan '13

Hi Sorry if these questions are obvious but I just don't know how to find the answers. I'm trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I've got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I've created workflow but don't know how to access this key. Also in the first example it states <galaxy_url>/api/workflows However I don't have the "api/workflows" directory structure in my galaxy-dist, do I need to create this? Thanks Neil

4 3

Login problems
by Jennifer Jackson 18 Jan '13

18 Jan '13

Myself and a co-worker are both having issues with uploading files on to our galaxy accounts through the FTP server. We can get our files transferred onto the FTP, but when we click "Get Data" and checkmark them to be loaded on the account, they sit indefinitely in the work queue. Both of us are having this issue on two separate accounts. Any idea what is going on with this? > > Thanks! > > Abhi

1 0

Tophat mapping and Cufflinks output issues
by Jim Cohen 16 Jan '13

16 Jan '13

Hello Galaxy Users- I've been using the Main Galaxy server to work on an RNA-Seq project for a non-model plant, and I've noticed that my output from Tophat and Cufflinks might not be as good as I'd like. I have a reference transcriptome assembled in Trinity, and it is based on the same Illumina-generated 100 bp reads I'm trying to map to it. When I use Tophat to map the reads to the reference transcriptome (I have trimmed the reads and filtered the lower quality ones), only about 10% of the reads actually map, so I go from 30,000,000 reads before mapping to 3,000,000 that are actually mapped. Therefore, I feel like I'm losing a lot of data. When I've changed the parameters to allow for more mismatches, not many more reads seem to map, and in many cases, the Tophat run fails and I receive the error message: "*Settings: Output files: "/tmp/ 3030460.cyberstar.psu.edu/tmpWbxTnm/dataset_5530451.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: def"*. I've had similar numbers of reads map with Bowtie by itself and BWA as well. I've also tried mapping the reads to the assembled isoforms (contigs) of the transcriptome, and this results in many more reads (close to 90%) being mapped. Therefore, I figure the reads should map to the reference transcriptome, and I'm not sure why this isn't happening. The other issue I've run into is that in Cuffdiff only about 4,800 genes appear in the output files as being tested for differential expression. There are approximately 100,000 genes in the reference transcriptome, so I was thinking that there should be more than ca. 4,800 that are tested for differential expression. Should each gene be tested? Does Cuffdiff just not report some of the genes that are not differentially expressed, or is the program not testing all of the genes? If anyone can provide some help, guidance, or a suggestion, I'd greatly appreciate it. Thanks, and take care. Jim

2 1

identify different number of differential expressed genes using ensemble or reseq GTF
by Wei Liao 15 Jan '13

15 Jan '13

Hi all, I am analyzing significant differential expressed genes for a pair of normal V.S tumor, using Cuffdiff 2.0.2. I noticed that by using ensemble GTF and refseq GTF, the results showed a big difference on the number of genes being significant expressed. For ensemble GTF, there are only 250 genes differential expressed. But for refseq GTF, there are about 1000 genes. I am running these data on Galaxy server and with the same workflow. Can anyone explain what is going on here? so which result should I trust? Thanks. -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645

3 3

Re: [galaxy-user] converting solid files
by Enis Afgan 14 Jan '13

14 Jan '13

Hi Nuphar, I believe yu should be using a tool that is color-space aware and not converting the data - Galaxy Main has 'Bowtie for SOLID' available, which should understand your data as is. BTW, for these types of questions, you should send the email to galaxy-user mailing list (http://lists.bx.psu.edu/listinfo/galaxy-user) which I have CC'd now, because that will get your question much more exposure and thus higher likelihood of a useful answer. Cheers, Enis On Sun, Jan 13, 2013 at 9:58 PM, Nuphar Salts <nupharsalts(a)gmail.com> wrote: > Hello, > > We're trying to convert csfasta and qual files to fatsq, using galaxy. > The problem is that it seems that A is always used as the first base, for > each number representing a color. > We want to use bowtie for analyzing RNA-seq results. > Is it possible to convert our files with galaxy or should we use another > tool? > > Thanks, > Nuphar. >

1 0

Uploading files to history via API
by Neil.Burdett＠csiro.au 14 Jan '13

14 Jan '13

Hi, It seems the API documentation is a bit scarce. I'd like to upload a file from the command line using the API rather than the GUI, but would like to see the file in the history. Does anyone have any information how to do this/ any tools that are available. Thanks Neil

1 0

Galaxy January 11, 2013 Distribution & News Brief
by Jennifer Jackson 11 Jan '13

11 Jan '13

*Galaxy January 11, 2013 Distribution & News Brief* <http://wiki.galaxyproject.org/News/2013_01_11_DistributionNewsBrief> * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11>* * Highlights:* * /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more... <http://wiki.galaxyproject.org/News/GCC2013TrainingDayNominations> or see http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay * XML defined Tool shed repository dependencies <http://wiki.galaxyproject.org/DefiningRepositoryDependencies> introduced * Various enhancements <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Other_Tool_Shed> to Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed> containers, display of README files and SVG images, and the tool shed's functional test framework <http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framewo…>. * New genomes <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Data> added to *Main <http://wiki.galaxyproject.org/Main>* Galaxy instance and rsync download. * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r a4113cc1cb5e / *Thanks for using Galaxy,* / The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

1 0

macs error for chipseq data
by Sun, Wenping [USA] 11 Jan '13

11 Jan '13

Dear galaxy users, I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: /bin/sh: macs: not found Anybody can kindly provide some hints? Thanks, Kathryn

2 2