October 2011 - galaxy-dev - lists.galaxyproject.org

SICER bug in Workflow
by Susan Newman 07 Dec '11

07 Dec '11

I'm working on a SOLiD ChIP-Seq workflow in which I want to use SICER for peak detection. In attempting to add SICER to the workflow, I've run into some difficulty: 1) My input is an interval file which I've created using Convert SAM. In order to connect to the SICER module, I had to use a trick by setting up the connection with the Convert SAM set to BED. The SICER algorithm fails to run when tested with the bed file. If I then change the connected Convert SAM to interval, SICER will run. 2) I need to change the default run parameters but they are not saved in the workflow. There is always reversion to the default values. I get a Server error notice. This workflow also contains Bowtie and MACS. Parameter changes for these algorithms are saved correctly. 3) I would like to run SICER twice in the workflow with different parameters. Is it allowable to load SICER a second time? May I run from the same interval conversion file? I tried this and again could not get the input file recognized as a valid connection. Thanks in advance, Susan Susan S. Newman, Laboratory Manager Genomics Core Facility, L2012 Pennington Biomedical Research Center 6400 Perkins Road Baton Rouge, LA 70808 225-763-0255 (o) 225-763-0257 (lab) http://gcf.pbrc.edu

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Job output not returned from cluster
by Joseph Hargitai 01 Dec '11

01 Dec '11

Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. thanks, joe

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FASTA manipulation!
by David PANG 29 Nov '11

29 Nov '11

Dear All, I am new to Galaxy! When I tried to manipulate mt fasta sequences from RNA-Seq, I just add >1, >2...........>1000000 etc! Right now, I am trying to add libraryA to all of the sequences like >libraryA_1, >libraryA_2.........>libraryA_1000000. I can not figure out how to do it on Galaxy. Could somebody help to this end. Thanks David -- David PANG, Ph.D.

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custom indexes
by Candace Seeve 29 Nov '11

29 Nov '11

I'd like to map RNA-Seq data from two different bacterial species to their genomes. How do I go about getting a custom index added to the galaxy server? One of the genomes is not yet published so is it possible to keep the indexes private? Thanks, Candace

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Integration with LIMS
by Sonderegger Bernhard 29 Nov '11

29 Nov '11

Hello, I am exploring the possibility of using a local galaxy installation for light bioinformatics on sequence data in the scope of an existing LIMS system. Ideally I would like to be able to do the following 1. Push datasets from the LIMS to galaxy (directly into the user's account or into a fresh temporary session) 2. Allow the user to perform tasks within galaxy, backtracking and retrying as necessary. 3. Push the results along with the galaxy history (ideally converted to a workflow) back to the LIMS 4. (Allow workflows stored in the LIMS to be pushed to Galaxy along with further datasets or even completely automatic launch of these workflows from within the LIMS) Is this feasible? How much wrok would be required? Since I am new to Galaxy (at least from the development side), I would very much appreciate comments advice and pointers to documentation or existing projects of a similar nature. Thanks in advance, Bernhard

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trannsfer files from remote system to galaxy
by shashi shekhar 29 Nov '11

29 Nov '11

Hi, In my local instance of Galaxy ,I want to add one option in which i can get files from remote system to galaxy in data library . except url is there any option to get remote files from galaxy ? Regards

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downloading bowtie indexed files
by Nikhil Joshi 29 Nov '11

29 Nov '11

Hi all, Just wondering if there is a way to download the bowtie indexed files after indexing. It seems that the indexed output is simply a meta-file that points to the directory where the indexed files are kept.... but what if I want to download all of the indexed files themselves? I wrote something to do this... basically I created an html page that is the output of bowtie-build which then points to the created files... but I'm wondering if there is an easier way...? - Nik.

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Name your own tool's output?
by Timothy Wu 18 Nov '11

18 Nov '11

Hi, I thought I had already asked this question a while ago, but I can't find it so I guess I haven't. When porting my own tool, is there anyway to customize the name of the output? Timothy

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Dataset Cleanup Question
by Lance Parsons 17 Nov '11

17 Nov '11

I am running a local instance of Galaxy and I've been trying to sort out some issue with dataset cleanup. For the most part, things are working OK running the shell scripts in the recommended order: delete_userless_histories.sh purge_histories.sh purge_libraries.sh purge_folders.sh delete_datasets.sh purge_datasets.sh I have the number of days set to 10. When I look at the reports webapp however, it reports that there are "62 datasets were deleted more than 15 days ago, but have not yet been purged, disk space: 12975717335." These have stuck around now for 45 days (and counting). I have even tried running the scripts with the -f option to force galaxy to re-evaluate the datasets to no avail. Any suggestions? Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Adding bowtie-build ONLY as its own tool
by Nikhil Joshi 10 Nov '11

10 Nov '11

Hi all, So I am trying to add a tool to our local Galaxy, for which it needs a bowtie-build indexed reference, but NOT the alignment. The alignment step is done by the tool itself (using bowtie). My question is two-fold: One, why does the bowtie tool do both indexing and mapping? It seems that you would want to have the indexing separate from the alignment so that you can index once and then align as many times as you need. Right now it seems like (correct me if I am wrong) that EVERY time you do an alignment, Galaxy will index the reference. This seems like it is adding a lot more time to the alignment step than is necessary. Is this correct, or am I missing something? Two, so if I were to make bowtie-build into its own tool, how could I access the files that it creates, i.e. since bowtie-build takes a reference and a prefix as input and then creates multiple files that use the prefix.... I guess I need to access the prefix name somehow.... any help would be highly appreciated. Thanks! - Nik.

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