User: y.hoogstrate

gravatar for y.hoogstrate
y.hoogstrate400
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400
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Netherlands
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4 days, 3 hours ago
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2 years, 11 months ago
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Posts by y.hoogstrate

<prev • 67 results • page 1 of 7 • next >
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Answer: A: STAR in multiple threads faces issues in opening genome file
... how much memory do you have in that machine? The Galaxy wrapper has set `--genomeLoad NoSharedMemory` (default STAR option). The consequence is that running two jobs in parallel, makes two copies of the reference genome (~30gb) in the RAM. Could this have anything to do with it? ...
written 5 weeks ago by y.hoogstrate400
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Answer: A: STAR in multiple threads faces issues in opening genome file
... Do you use references genomes from history or from Galaxy's cache and are you running STAR on identical or Different references? ...
written 5 weeks ago by y.hoogstrate400
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Comment: C: User Tool Does Not Initialize
... This is where work starts to become fun ;) ...
written 8 weeks ago by y.hoogstrate400
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Comment: C: User Tool Does Not Initialize
... Did you configure it in `./config/tool_conf.xml` with the correct PATH (relaltive to ./tools/, and the XML within there? ) or install via a toolshed? ...
written 9 weeks ago by y.hoogstrate400
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Answer: A: User Tool Does Not Initialize
... ``` Phylip format AXT format ``` This needs options - https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-option Phylip format AXT format ...
written 11 weeks ago by y.hoogstrate400
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Answer: A: Changing the command syntax of a tool in xml (changed are not applied)
... Planemo makes development very easy: http://galaxyproject.github.io/training-material//Dev-Corner/slides/tool_integration#41 ...
written 11 weeks ago by y.hoogstrate400
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Comment: C: User Tool Does Not Initialize
... I can interpret your question in 2 ways: (1) `planemo serve` starts, but does not load your tool. This usually means the tool is not correct. What does `planemo lint` tell you? If you're stuck, please drop the latest version of your tool XML and i'll have a quick look at it. (2) `planemo serve` star ...
written 11 weeks ago by y.hoogstrate400
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Comment: C: User Tool Does Not Initialize
... Choose the paths relative to the test-data directory. For a tool with the following directory structure: ``` ├── hisat2_macros.xml ├── hisat2.xml ├── test-data │   ├── hisat_input_1_forward.fastq │   ├── hisat_input_1_reverse.fastq │   ├── hisat_input_2_forward.fastq │   ├── hisat_input_2_reverse.f ...
written 12 weeks ago by y.hoogstrate400
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Comment: C: Mapping quality plot of BAM file
... Oops, that should be possible too. Convert to SAM and exclude the header, use `cut` in Galaxy to pick column 5 (https://samtools.github.io/hts-specs/SAMv1.pdf, sec 1.4) and visualize this in Galaxy Charts. ...
written 3 months ago by y.hoogstrate400
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Answer: A: Mapping quality plot of BAM file
... Hi there, You can use `samtools view` (in Galaxy as the following tool **Filter SAM or BAM** *, output SAM or BAM files on FLAG MAPQ RG LN or by region*) to subselect the region. With that alignment you can go back to FASTQ and : - Then dump the BAM to FASTQ (FastqToSam convert Fastq data into u ...
written 3 months ago by y.hoogstrate400

Latest awards to y.hoogstrate

Scholar 5 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 6 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 6 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 6 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Supporter 11 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 14 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Is HISAT2 working in GALAXY?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Making PNG figures from plots in R from toolshed (without X11)

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