Question: Error installing/using 'data_manager_fetch_genome_dbkeys_all_fasta'
1
gravatar for fiebig
8 months ago by
fiebig30
fiebig30 wrote:

Hello, in order to prepare some reference genomes for visualisation module, I have installed the following data manger: 'data_manager_fetch_genome_dbkeys_all_fasta'.

No errors were reported during the installation. When I clicked "Local data" the data managers were present. My previously populated "all_fasta.loc" file was recognized and included.

Nevertheless, I'm not able to include my data. When clicking "Create DBKey and Reference Genome", a tab in the browser opens, showing a white label: "Tool request failed.Uncaught error."

I had a closer look in the repository and thereby found the following error: "Dependency was not resolved by any resolver module." I have already removed and re-installed the tool, but the error remains. What might be the problem here? I'm I bit confused, since I already have been able to install tools from the toolshed successfully.

I run a local instance with the latest galaxy version.

Regards, Anne

software error • 182 views
ADD COMMENTlink written 8 months ago by fiebig30

Are you still having this problem or has it resolved? I tested this tool just last Friday on a 16.04 default local and it worked fine.

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson21k

The actual “problem” is not solved yet, but I have been able to supply trackster with the dbkeys/seq-/len- data via the different .loc files. It might be more convenient to use the data managers, but I’m fine with the import now.

Unfortunately I encountered another problem using trackster. While I try to load a bam file to my yeast file in trackster, I get the following error: Convert BAM to BigWig on data 139 /galaxy_DB/job_working_directory/000/372/tool_script.sh: line 9: bedtools: command not found needLargeMem: trying to allocate 0 bytes (limit: 100000000000)

Here is the command from the above tool_script.sh: “bedtools genomecov -bg -split -ibam /galaxy_DB/files/000/dataset_873.dat -g /galaxy/tool-data/arxula/len/Arad1.chr.len > temp.bg ; bedGraphToBigWig temp.bg /galaxy/tool-data/arxula/len/Arad1.chr.len /galaxy_DB/files/000/dataset_875.dat”

I can execute the command as user “galaxy”. Bedtools and the UCSC tools are in the PATH and can be used successfully in galaxy apart from the visualisations. What might be the problem here? Are there any recommendations according the RAM needed?

Anne

Von: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Gesendet: Montag, 1. August 2016 23:41 An: Anne Fiebig Betreff: [galaxy-biostar] Error installing/using 'data_manager_fetch_genome_dbkeys_all_fasta'

Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org

User Jennifer Hillman JacksonJennifer Hillman Jackson wrote Comment: Error installing/using 'data_manager_fetch_genome_dbkeys_all_fasta'C: Error installing/using 'data_manager_fetch_genome_dbkeys_all_fasta':

Are you still having this problem or has it resolved? I tested this tool just last Friday on a 16.04 default local and it worked fine.

ADD REPLYlink written 7 months ago by fiebig30
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