- galaxy-user - lists.galaxyproject.org

Cleanup script error - guess_dialect_for_url
by rocco.piazza 26 Mar '12

26 Mar '12

Hello, I'm working on a local instance of Galaxy-dist and I just updated it. Right after the update I tried to run the cleanup scripts. Unfortunately what I'm getting is the following error: # sh delete_datasets.sh -d 0 -r Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 101, in main app = CleanupDatasetsApplication( config ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 512, in __init__ self.model = galaxy.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False, object_store=self.object_store ) File "/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py", line 1818, in init load_egg_for_url( url ) File "/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py", line 1798, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py", line 1794, in guess_dialect_for_url return (url.split(':', 1))[0] AttributeError: 'bool' object has no attribute 'split' The same error occurs if I try to run other cleanup scripts, such as the delete_datasets or purge_datasets. Any idea to solve this issue? Best regards, Rocco

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How can I sort BAM/SAM file by read names?
by Carlos Borroto 26 Mar '12

26 Mar '12

Hi, I need to sort a BAM file by read names, I was wondering if this is possible with a tool included in Galaxy? I know any BAM file produced inside Galaxy will be sorted by coordinates, but I couldn't find an option to change this to queryname in any tool. Picard has the tool SortSam[1], perfect for this task, but it doesn't seem to be included at the moment. Is there any other option currently included? Are there any plans to include one? [1]http://picard.sourceforge.net/command-line-overview.shtml#SortSam Thanks, Carlos

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Chip-seq exercise
by Joshua Udall 25 Mar '12

25 Mar '12

Does anyone know what happened to the chip-seq exercise by James? It was part of a collection here: http://main.g2.bx.psu.edu/u/james/p/exercises and it was linked here: http://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq But is it 'Not Found'. It was a very useful exercise. Will it be back soon? Josh

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Reference genomes at local instance of Galaxy
by Yang, Yanming 23 Mar '12

23 Mar '12

Hi, I have just installed a Galaxy instance at my local machine and uploaded some sequence data into it. But, when I tried to use some NGS tools which need reference genome, I found the selection window was empty. I wonder how to get a reference genome data (e.g., hg19) incorporated into the local Galaxy. Any help will be greatly appreciated. Thanks! Yanming Yang

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Table with gene count reads
by Luciano Cosme 23 Mar '12

23 Mar '12

Hi, I was wondering if there is any tool on Galaxy were I can obtain a table with how many reads have been mapped to a given sample and to a given gene (for example, use a Tophat output and use a GFF file to obtain the table). I am using HTSeq to get it (htseq-count). There is also GenomicRanges and easyRNASeq packages in bioconductor. Thank you. Luciano

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problems with color settings in Visualizations
by Mackenzie Gavery 22 Mar '12

22 Mar '12

Hi, I am working with some saved visualizations, and finding that the color settings are not working today. Specifically, every time I change the color (in Settings) the result is the feature ends up black regardless of the color selection. Could you help me with this issue? Thanks, Mackenzie

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Subdivide peaks
by Mónica Pérez Alegre 22 Mar '12

22 Mar '12

Hi I´m working with data from tiling array (S.cerevisiae). I need to analyze the distribution of the enrichment signal along the length of all ORFs. So I want subdivide the genomics intervals into 10 segments independent of ORF size. Are there any tools in galaxy for this? Thanks for the helpful Regards ☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications Mónica Pérez Alegre, PhD Genomics Unit CABIMER-CSIC Edif. CABIMER - Avda. Américo Vespucio s/n Parque Científico y Tecnológico Cartuja 93 41092 Seville-SPAIN Tlf: +34 954 467 828 Fax: +34 954 461 664 www.cabimer.es<http://www.cabimer.es/> http://www.cabimer.es/web/es/unidades-apoyo/genomica

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"Job is waiting to run"
by Shisheng Li 22 Mar '12

22 Mar '12

Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as "Job is waiting to run" forever. The total volume of my files is 249 mb, which is far below the quota limit of 250 gb, and I am trying to run less than 8 jobs. Could you please let me know the possible reasons? Sincerely, Shisheng

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Drosophila yakuba reference genome
by Evgeny Brud 21 Mar '12

21 Mar '12

Hi, Could galaxy include the Drosophila yakuba reference genome for use with Tophat? It's not listed.

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Bowtie Seed length (-l) and non-unique reads mode (m=-1)
by Eric Guo 21 Mar '12

21 Mar '12

Hi there, I have two questions regarding alignment using Bowtie: 1. Is there a way to set the Seed Length (-l) to the full length of each read instead of using a single Seed Length for all reads? 2. When using m = -1 mode (Suppress all alignments for a read if more than n reportable alignments exist (-m): OFF), will a read be randomly assigned to one of the alignment positions in the genome? Or, will all the alignments for one single read be reported in the final output .bam file. Thanks in advance for your help. -Eric

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