User: testtoolshed

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testtoolshed10
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Posts by testtoolshed

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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 6 days ago by testtoolshed10 • updated 6 days ago by Jennifer Hillman Jackson22k
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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 19 days ago by testtoolshed10
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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 8 weeks ago by testtoolshed10
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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 8 weeks ago by testtoolshed10 • updated 8 weeks ago by Jennifer Hillman Jackson22k
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Answer: A: Bioconda for R-tool dependencies
... Thank You Bjoern, I will try that ...
written 8 weeks ago by testtoolshed10
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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 9 weeks ago by testtoolshed10
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download.file function error
... Hello, I have been trying to wrap R-based tool to download data from GEO database and I have tried different methods (wget, curl, libcurl, auto) and still get same error. None of these work. Do you have any idea what I'm doing wrong or maybe someone have same issue with "download.file" function? Fa ...
R download.file written 9 weeks ago by testtoolshed10
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Answer: A: This repository requires dependencies that cannot be installed through the Tool
... Thank you, it's work now :) ...
written 6 months ago by testtoolshed10
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Answer: A: This repository requires dependencies that cannot be installed through the Tool
... Hi, It's getGEO tool and his dependency repository methyldata1_16_2: https://toolshed.g2.bx.psu.edu/view/testtool/get_geo/73cd17bea9c4 https://toolshed.g2.bx.psu.edu/view/testtool/methyldata_1_16_2/ea44a0861444 I have same issue with both of them and really short requirements section: methy ...
written 6 months ago by testtoolshed10
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This repository requires dependencies that cannot be installed through the Tool Shed
... Hello, I am facing problem when I am trying to publish my new tool on tool shed. Everything work on my own instance but when I create public repository It's showing error: This repository defines tool requirements that cannot be installed through the Tool Shed.Please activate Conda dependency reso ...
requires dependencies tool shed written 6 months ago by testtoolshed10

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