User: testtoolshed

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testtoolshed30
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4 months ago
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Posts by testtoolshed

<prev • 14 results • page 1 of 2 • next >
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Comment: A: WARNING:galaxy.model:Datatype class not found for extension(...)
... Yes, I've binary.py file with idat as well what else I can try to make it work? ...
written 6 months ago by testtoolshed30
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WARNING:galaxy.model:Datatype class not found for extension(...)
... When I test my tool I get the error: **WARNING:galaxy.model:Datatype class not found for extension 'idat'** I've checked galaxy datatypes and idat is one of them. Could you please help me with this issue? ...
idat config datatype datatypes_conf.xml.sample written 6 months ago by testtoolshed30
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Custom tool: loading data from base dir
... Hi, If I want to create tool loading data from base dir in this case It would be galaxy history "dir" can I provide path to it somehow or are you recommended some other way of doing it? ...
input base dir development tool tool_comf.xml written 6 months ago by testtoolshed30 • updated 6 months ago by Jennifer Hillman Jackson25k
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Planemo tool_init input options
... Hi, Is it possible to add labels and "type in" (number/txt) or "pull down menu" input using planemo tool_init command? ...
input tool planemo written 7 months ago by testtoolshed30
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New tool error - could not find function from (R) bioconda package
... Hi, I've tried to develop new tool based on getGenomicRatioSetFromGEO function from bioconductor-minfi package. It works for me on my computer but didn't work on galaxy and return *Fatal error: Exit code 1 () Error: could not find function "getGenomicRatioSetFromGEO" Execution halted* Is it R vers ...
R new tool bioconda error written 13 months ago by testtoolshed30 • updated 13 months ago by Jennifer Hillman Jackson25k
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Comment: C: Bioconda for R-tool dependencies
... Hi, I contribute r-rentrez on bioconda and received fatal error on galaxy: *Exit code 127 () /srv/galaxy/server/database/jobs/006/6814/conda-env/lib/R/bin/exec/R: symbol lookup error: /srv/galaxy/server/database/jobs/006/6814/conda-env/lib/R/bin/exec/../../lib/../../libreadline.so.6: undefined sym ...
written 13 months ago by testtoolshed30
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Answer: A: download.file function error
... Hi Hans-Rudolf, I try today and have this error again. It is same with other scripts based on "download.file" function (GSE, GSM accession doesn't matter). They used to work before and on my local galaxy. I checked my scripts and xml few times just in case and everything looks fine (no R errors or ...
written 15 months ago by testtoolshed30
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HISAT2 gzip: input_r.fastq.gz: not in gzip format
... Hello, I have been trying to use HISAT2 to to align RNA-seq ENCODE data which I download on my device and try upload by filesystem paths as dataset in data library (they are .fastq.gz files) but after loading them I received .fastq files and as a result error in HISAT2 gzip: input_f.fastq.gz: not in ...
hisat2 gzip rna-seq written 15 months ago by testtoolshed30 • updated 15 months ago by Jennifer Hillman Jackson25k
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Answer: A: Bioconda for R-tool dependencies
... Thank You Bjoern, I will try that ...
written 15 months ago by testtoolshed30
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Bioconda for R-tool dependencies
... Hello, I have been trying bioconda for R-tool dependencies for few of packages It is work perfectly but one of my tool need rentrez package (I've tried entrez-direct but I think It is something bit different). What should I do in that case? I've normally use this website for dependency https://bioco ...
R bioconda dependencies written 15 months ago by testtoolshed30

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