- galaxy-user - lists.galaxyproject.org

Can we continue the workflow from some of the steps?
by Cinto Queky 24 Oct '11

24 Oct '11

Hi All, Supposed we ran into some problems with some of the steps in a workflow, and would like to continue to run from those steps after correcting it, can we do that? Right now, we have to re-start the whole workflow. Thanks. Cheers,Cinto

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tool config file: multi-select for files?
by Appelt, Uwe 21 Oct '11

21 Oct '11

Dear all, My tool does accept multiple input-files, but there are normally bunches of them, so the "repeat"-syntax doesn't appear to be a good idea. Inspired from the workflow-engine-capability to accept multiple input files I wanted to do the same for my tool: <param name="inputSeqFiles" type="data" format="fasta" multiple="true" ... /> Problem: The above "param"-syntax causes Galaxy to caugh up an error message, as soon as I indeed select multiple files. Selecting single files works well. The, to actually access the list of selected files, I would expect the same syntax as for the "repeat"-tag case to work. What I am currently trying from within a <configfile>-section is something like this: #for $inputSeqFile in $inputSeqFiles ...do something with $inputSeqFile #end for Problem: Cheetah complains about $inputSeqFiles not being iterable. Any suggestions or ideas/alternatives to this setting? Thanks in advance and best regards, Uwe

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one error while installing galaxy
by Li, Jilong (MU-Student) 21 Oct '11

21 Oct '11

Hi, When I installed galaxy, one error message appeared, which said that ImportError: No module named distutils.util Fetch failed. Could you tell me how to solve this problem? Thank you very much!

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How to use Galaxy
by Boaz iga 21 Oct '11

21 Oct '11

Hi Folks, I am just beginning to use galaxy and was wondering whether besides the tutorial video there are other user guide materials/documents I can find. I need some kind of a user manual but can't see it. Anyone who know's where this is please help. Will be grateful to read from you. Boaz.

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Get only repeatmasked exons
by Managadze, David (NIH/NLM/NCBI) [F] 21 Oct '11

21 Oct '11

Dear Galaxy expert(s), I have .BED file of regions from mouse. I guess many of them can span whole genes i.e. many exons; might even span over the gene flanks. I need to get the REPEATMASKED sequences of only the annotated exons of these regions. I see that If I use the tool "Fetch Sequences->Extract Genomic DNA" on these regions, it returns sequences with mixed small and capital letters. Question I: what are the small letters and what are the capitals here? Are these already masked, exons/introns or what? (I downloaded some of these sequences and repeatmasked myself. My pasked sequences overlap with some of "yours" written in small letters.) Question II: Is the strand "honored" by these tool? I guess I remember from my old experience that there was an issue although I can not recall what exactly. Thank you in advance, David

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save/export image from workflow editor?
by Casey Bergman 21 Oct '11

21 Oct '11

Dear Galaxy Team - [Apologies if this has been answered before on this list before...I couldn't find anything related via google] Is there a way to save/export an image of the workflow shown in the workflow editor? Best regards, Casey

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Issue about uploading data
by Nandan Deshpande 21 Oct '11

21 Oct '11

Hi, My user id is "deshpandenandan1975(a)gmail.com". I have been trying to upload 2 files each around 650 MB in size but the upload is in process for last 15 hrs .. I had a similar problem in uploading data to Galaxy few months back and had to give up using the tool. Can u suggest me a way out? cheers, Nandan

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Zoom function on workflow editor?
by Arthur Goldberg 20 Oct '11

20 Oct '11

Hi Galaxy's cool! Is there a zoom function on the workflow editor? (I know about hiding nodes from the tutorial <http://main.g2.bx.psu.edu/galaxy101>.) Thanks Arthur -- Senior Research Scientist Computational Biology Memorial Sloan-Kettering Cancer Center cBio Cancer Genomics Portal <http://www.cbioportal.org/>

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bed12 format for stitching blocks given a set of coding exon intervals
by Amit Indap 20 Oct '11

20 Oct '11

Hi Galaxy, I am trying to stitch together MAF alignments for the coding sequence for a few genes of interest in Drosophila. I used UCSC to send the bed intervals of the coding exons of my gene and sent the output to Galaxy. But when I try and use the tool "Stitch Gene blocks" it complains that my bed is a bed3 and not a bed12. I'm a bit rusty with my browser skills, but how can I send my output to Galaxy as a bed12 format so I can stitch my MAF blocks together? Thanks for your help! Amit -- Amit Indap

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Query regarding RNA-Seq data analysis
by santhi ramachandran 19 Oct '11

19 Oct '11

Hi, I am having a fastq file for my RNA data analysis in my computer. How to make it available for RNA seq data analysis using tophat. Sandy

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