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

Question about Extract intron sequences from [gtf file] + [genome FASTA file]
by 师云 20 Aug '13

20 Aug '13

Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file]; Here is a simple of a gtf file: 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; I want to extract intron from the [gtf] file. I found 2 ways may solve the question but it is both useless; 1. I use (Filter and Sort) -> Filter to cut the [gtf] file into 2 files such as the follows: File A ( contain transcript ): 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; File B ( contain exon): 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; Then I use (Operate on Genomic Intervals)->Subtract to subtract File B from File A Return Non-overlapping pieces of intervals. I thought it will return a file containing intron But the result is an empty file; 2. I convert [gtf] file to [Bed] file ,and use (Extract Features)->Gene BED To Exon/Intron/Codon BED, and it return the same result, an empty file. I think it must be something wrong with my thoughts. So I really need your help. Thank you very much. sincerely yours, John

2 1

customize tool display in the workflow
by Jun Fan 19 Aug '13

19 Aug '13

Dear Galaxy develop team: Normally I generate the workflow from history. It works fine except one annoying problem: the display of step/tool is just the tool name, which can cause confusion in a big workflow. For example, I have a mixture of samples from multiple species and do the BLAST against Human, Virus, Mouse etc which will call BLAST several times. To make results distinguishable, I will rename the dataset in the history. But this will be lost when creating workflow from history. The workflow will have duplicate steps named as BLAST while I really want to have steps displayed as BLAST against Human etc. Could you tell me whether I have done something wrong? If not, could you kindly add this functionality into the new release of Galaxy? If it is possible to customize the tool display in the workflow, how to write the wrapper as setting the label to allow this? Best regards! Jun

2 1

Questions about column output in Operate on genomic Intervals -> Profile Annotations
by James Wagner 19 Aug '13

19 Aug '13

Hello, I tried using this tool today after inputting a bed file containing 1509 intervals of 100 bp each, spread across all 22 autosomes. First of all, despite the fact that my input file contained intervals for 22 chromosomes, the value of "allCoverage" seemed to be the same as the value of the coverage of that table only for chr1. I was not really sure about the tableRegionCoverage column, as for most of the autosomes I had input data spread throughout the chromsome with points a few Mb away from either end, but I was getting a value in this column only about 1/3 of what I get when downloading the data directly from UCSC and summing the interval sizes. There were also many cases where nrCoverage > allCoverage, even when I reduced each input genomic interval to only 1 bp to avoid redundancy in the input file. Based on these descriptions of the columns I would expect allCoverage >= nrCoverage at all times. Just wondering if you could clarify what these columns are supposed to mean or how to reconcile these apparent inconsistencies.

2 3

Uploading via FTP problem
by Delong, Zhou 19 Aug '13

19 Aug '13

Hello, I'm trying to upload some files via filezilla since Thursday and each time it fails after five or six hours of transfering and I cannot resume the transfer.. Every time I have the same errors: Status: Connection established, waiting for welcome message... Error: Connection timed out Error: Could not connect to server Each time it failes at different point so I don't think it's related to my files. Nor to the connection to the server, for I successfully downloaded some output data from the server (4 files, one of them was 20G). Is anyone experiencing the same problem or have an opinon on what's going on? Thanks, Delong

2 1

Is anyone using Galaxy with NeuroScience ?
by Zeeshan Ali Shah 19 Aug '13

19 Aug '13

Hi, Is any one using galaxy for Neuroscience and brain imaging ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

3 3

Questions regarding Galaxy Tool XML File
by Marian Thieme 16 Aug '13

16 Aug '13

Hi, I am working on a project to automate workflow generation and its execution and I found the XML tool config schema kind of interesting, in order to properly specify a tool interface. However, if I understand it right, the idea of the XML tool config is to provide a description of the galaxy graphical user interface rather then a general description of the actual tool's interface. So I started to write an XSLT to transform the galaxy tool config to another xml, which I believe, better fits my needs. In order to achieve this, I have a few questions: - param tag: I havent really understood how you define a parameter to be mandatory or optional. I see when it is the child of the repeat element that there is (maybe) a minimum defined. But when this is not the case, how can I conclude that the parameter is optional vs. mandatory ? - param tag's help attribute: can I assume any format, or is it simply the output of the tools help command ? - when do you update the tools and in turn the XML configs. (e.g. the gatk stuff is kind of outdated: 1.4 vs 2.6 ) Thanks, Marian

1 0

Name workflow output dynamically on input name
by Daniel Gorelik 14 Aug '13

14 Aug '13

Hello, I have been just getting the hang of workflows and finding them very useful. I have one question, though. Is there any way to name an output of a workflow dynamically based on the input? Thank you, Daniel Gorelik dgorelik(a)bu.edu

2 1

Re: [galaxy-user] Egg build failed for numpy 1.6.0
by Fabrice BESNARD 14 Aug '13

14 Aug '13

Hi, I am preferentially using the main server. But recently I have also tried to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8). Since I am not a specialist at all, I asked some kind of "expert" people from my institute. They told me that installing Galaxy on Mac can really be nightmare because there are some conflicts in the versions of python... This could explain the problem you are encountering with the egg dependencies. So they advised me to install an Ubuntu (12.04) operating system in a virtual machine using Virtual box. This is supposed to be much easier to install Galaxy and indeed, the installation of my local galaxy server ran fast and well. However, I don't know whether the tip is good or not, because I am now facing big problems with the virtual machine: the Ubuntu virtual machine is very unstable and often crashes while running big datas on Galaxy... The problem does not come from Galaxy, but from either Ubuntu guest system, the virtual machine or the communication with the mac host system and I haven't found out how to fix it yet. But since your version of Mac is different, you can try this solution, it might work better in your configuration. Hope that helps, Fabrice But at the moment, I have lots of problem with the > Hi, > I am trying to install a local version of galaxy on my mac book (x86_64, OSx 10.8.4). I seem to be having a lot of trouble with fetching and installing specific egg dependencies. Initially pysam was giving me trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now I have trouble with the numpy egg dependency. Does anyone have any idea > why a egg would fail to build. I am assuming it is because I have a more recent numpy version (1.7.1) installed already. What should I do, short of > uninstalling the newer version of numpy ? > Any help on the matter would be greatly appreciated. > Thank you. > L > -- > =================================== >>Dr. Lahcen Campbell < >>Contact: lahcencampbell(a)gmail.com < >>http://bioinf.may.ie/index.html < > =================================== > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > http://lists.bx.psu.edu/listinfo/galaxy-dev > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > http://lists.bx.psu.edu/ > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

2 1

ftp access on https://test.g2.bx.psu.edu/
by Amit Pande 14 Aug '13

14 Aug '13

Hi, Kindly allow the ftp access to work ....I want to upload big files....not working... regards, Amit.

2 1

adding reference genome
by Vijay Kumar 14 Aug '13

14 Aug '13

Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u

2 1