- galaxy-user - lists.galaxyproject.org

Problem setting up admin in Galaxy local instance!
by Di Nguyen 21 Jul '12

21 Jul '12

Dear all, Please help me figure out what went wrong to set up ADMIN in my local instance using the new retinaMBP! This is what I did 1. I changed universe_wsgi.ini.sample file into universe_wsgi.ini (using Mac TextEdit) 2. Then, I edited universe_wsgi.ini as followed: # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = *dknguyen(a)uw.edu* 3. I shutdown Galaxy, rerun sh run.sh, log back in Galaxy but still no Admin function. 4. The reason that I wanted to ad Admin function is to import my NGS files (bigger than 2Gb fer sure) into Galaxy database. Please give me some tips on this as well. Thank you very much, Di Nguyen, postdoc U of Washington, Seattle, WA

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cuffdiff failed
by i b 21 Jul '12

21 Jul '12

Hi, I had 3 samples (2replicates treated (A-B) and one untreated (C) ). I did cufflnks and cuffmerge (all 3 cufflinks) I run cuffdiff with the following options: cuffmerge + tophats from A, B, C (2 groups: gr.one with A, B), gropu2: C. I had the following message: 0 bytes An error occurred running this job: cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.050000 -N -b /galaxy/data/hg19/sam_index/hg19.fa --labels + /galaxy/main_pool/pool4/files/004/645/dataset_4645857.dat /galaxy/main_pool/pool3/files/004/623/dataset_4623286.dat,/galaxy Where did I do wrong? What does it mean? Cheers, ib

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Attempting to use parallelism in BWA
by Kevin C. Dorff 20 Jul '12

20 Jul '12

Hi, I am using Python 2.7. I am running with an hg checked out, up to date version of "https://bitbucket.org/galaxy/galaxy-dist/". I am very new to Galaxy. I have an instance setup *and running* locally. I am able to perform routine actions such as uploading files, processing with Picard, and aligning with BWA. I have been able to make the jobs execute out our SGE cluster. In order to better utilize my cluster, I attempted to enable parallelism of the tasks that support it (such as BWA) by configuring the * universe_wsgi.ini* file with the parameter use_tasked_jobs = True When I do this and attempt execute a BWA alignment on a 4.1Gb fastq file, I am given the error Result 256 from mv /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 25, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py", line 13, in ? import galaxy.datatypes.registry File "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py", line 146 finally: ^ SyntaxError: invalid syntax The alignment failed. If you need the complete error message, contact me and I can supply you with it. It's too large to paste in-line and attachments aren't allowed. Is there more I need to do to enable parallel jobs (splitting of input, align, then merge)? Any suggestions are greatly appreciated. Kevin

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extracting, stitching, converting MAF files: interval_maf_to_merged_fasta.py: command line usage?
by Anton Kratz 20 Jul '12

20 Jul '12

Dear Galaxy team / user mailing list, my question is with respect to command line usage, not about interactive / web-based Galaxy usage. Regarding the publication [1], section "2.3 Stitchers". I want to use the stitcher to extract a given region from MAF files, stitch it together and convert it to FASTA. I downloaded and installed Galaxy according to the instructions from http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the /tools/maf directory (not clear from the paper or docs but I belive this is the tool that implements this functionality). How can I actually extract, stitch, convert with interval_maf_to_merged_fasta.py? I have difficulties figuring all necessary command line parameters out by reading the source code. F.e. here I tried to get the stiched FASTA conversion for a region defined in "foo.bed" out of "chr1.maf": $ python ./tools/maf/interval_maf_to_merged_fasta.py -G -i ../foo.bed -m ../chr1.maf -d hg18 -o stdout Traceback (most recent call last): File "./tools/maf/interval_maf_to_merged_fasta.py", line 196, in <module> if __name__ == "__main__": __main__() File "./tools/maf/interval_maf_to_merged_fasta.py", line 107, in __main__ if options.mafSourceType.lower() in ["cached"]: AttributeError: 'NoneType' object has no attribute 'lower' Is it necessary to index the MAF files first somehow? Do I have to set the type of MAF file, and to what? Would be great if someone could give a short overview how to stitch MAF files command-line based. Thank you! Anton References [1] Blankenberg, D., Taylor, J., Nekrutenko, A. & Galaxy Team. Making whole genome multiple alignments usable for biologists. *Bioinformatics (Oxford, England)* *27*, 2426-2428 (2011)

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Error in mapping with bowtie
by Hongkyun Kim 20 Jul '12

20 Jul '12

Hi Experts! I uploaded my data (two pair-end fasq files from illumina), processed with fasq groomer, and then mapped processed data using a reference genome with Bowtie. I got strange errors I cannot possibly understand. None of the files have ind, wped, wsf, or wpf. Any idea? WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'ind': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wped': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wsf': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wpf': 'module' object has no attribute 'wsf' Thanks in advance.

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cuffdiff results missing
by i b 20 Jul '12

20 Jul '12

Hi, I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group one has two replicates (treated) and group two only one replicate (untreated). When looking at the outputs the following are empty (1 line): TSS group FPKM tracking TSS groups differential expression testing CDS FPKM tracking CDS FPKM differential expression testing CDS overloading diffential expression testing promoters differential expression testing splicing differential expression testing the other four outputs have data downloadable as excel. Is this normal? thanks, ib

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quota limit
by Hongkyun Kim 19 Jul '12

19 Jul '12

Hi there, I am a newbie at Galaxy (registered last night), and have been given 10Gb space. I wonder whether I can increase quota size somehow. I have just uploaded two related files (each 3Gb), and then converted one file to a new format (another 3Gb). Now, I cannot do anything.

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Galaxy intro webinar
by wlathe 19 Jul '12

19 Jul '12

Greetings all! We will be giving a 1 hour 15 minute Intro to Galaxy webinar tomorrow (Thursday, July 19th) at 11am PDT, 2pm EDT. Registration is open and free. Registrants will also have access to a recording, slides and exercises. The webinar will go through the basics of using Galaxy, tools, histories and workflows. If you'd like to attend or would like to see more information, check our our webinar registration page: http://www.openhelix.com/cgi/webinars.cgi Trey (OpenHelix)

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Post
by Rachael Sirois 18 Jul '12

18 Jul '12

rsirois(a)smith.edu

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cuffcompare outputs missing
by i b 18 Jul '12

18 Jul '12

Hi, I ran cuffcompare using 3 samples as inputs (dataset 1-2-3 cufflinks gtf) and a reference annotation (dataset 4). These are the outputs: 5: Cuffcompare on data 1, data 4, and others: transcript accuracy 6: Cuffcompare on data 1, data 4, and others: 1 data tmap file 7: Cuffcompare on data 1, data 4, and others: data 1 refmap file 8: Cuffcompare on data 1, data 4, and others: data 2 tmap file 9: Cuffcompare on data 1, data 4, and others: data 2 refmap file 10: Cuffcompare on data 1, data 4, and others: transcript tracking 11: Cuffcompare on data 1, data 4, and others: combined transcripts my question: why I don't have tmap and refmap on dataset 3?Why only 1 and 2 (arbitrary???) Thanks, ngs-ib

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