User: colindaven

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colindaven0
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Posts by colindaven

<prev • 9 results • page 1 of 1 • next >
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Answer: A: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... Try copying instead of linking ? I have never had good experience with linking ln -s and the webserver user - limited access - behind jbrowse. Also, are you looking in the right region where data is present ? ...
written 15 days ago by colindaven0
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Comment: C: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... This is how you set up a vcf in JBrowse. * x.vcf First bgzip * x.vcf.gz Then tabix * x.vcf.gz.tbi http://gmod.org/wiki/JBrowse_FAQ#How_do_I_set_up_a_VCF_file.3F ...
written 17 days ago by colindaven0
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Answer: A: STAR parameters in plants genomes
... STAR worked very well for me on hundreds of plant transcriptomes across about 10 species. I used 2pass mode instead of integrating the annotation, as non-arabidopsis annotation tends to be fairly poor, especially for lowly expressed transcripts. Otherwise the intron size parameter was fairly key a ...
written 4 months ago by colindaven0
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Answer: A: Assembling PE reads with broad fragment length distribution
... Sounds tough. I like soapdenovo2 (install via bioconda), since it is easy to configure and runs quickly. Another good assembler is Abyss. I think you'll have to try a lot of assemblies to get something usable since the sample sounds poor. ...
written 5 months ago by colindaven0
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Answer: A: Tools for error correction and data normalisation
... Hi Samdkhot, as far as I know, there are no read error correction programs on the Galaxy site (just checked the toolshed). ARe you looking to correct Illumina reads ? Have you checked the bioconda site to see if any are present there ? That would at least make them easier to install. https://bioco ...
written 5 months ago by colindaven0
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Comment: C: GALAXY_SLOTS and slashes
... Great post. I've had similar issues with SLURM on docker galaxy which are only partially resolved. ...
written 5 months ago by colindaven0
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Comment: C: Obtaining a tools.yaml to create a new galaxy docker flavour
... Hi Björn. Ok, unfortunately I can't get it to work. /data/rcug/galaxy_docker_preprot/tool_lists/ephemeris/ephemeris$ > ls common_parser.py generate_tool_list_from_ga_workflow_files.py __init__.py setup_data_libraries.py sleep.py common_parser.py.bak get_tool_list_from_ga ...
written 5 months ago by colindaven0
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Comment: C: Obtaining a tools.yaml to create a new galaxy docker flavour
... Hi Björn, I want to do the first option, to extend a Galaxy flavour. I think I can solve it myself, using the api. From this link I can get a JSON of the tools, then hopefully convert to yaml with a Python script https://usegalaxy.org/api/tools Thanks for your help, Colin ...
written 6 months ago by colindaven0
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Obtaining a tools.yaml to create a new galaxy docker flavour
... Hi, we are running the galaxy-rna-workbench docker galaxy which is very nice. We would like to extend this with new tools and especially data-managers and later workflows. In this document ( we're not using GKS quite yet) its documented how you can create a tools.yaml file from an existing well c ...
galaxy written 6 months ago by colindaven0 • updated 6 months ago by Bjoern Gruening4.8k

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