User: Peter van Heusden

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6 years, 5 months ago
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p**@sanbi.ac.za

Posts by Peter van Heusden

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Upload fastq to 'Data Libraries' Using Bioblend Python library
... What is the "something else" that it creates in the data library when you select to paste links? ...
written 2.2 years ago by Peter van Heusden150
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Answer: A: failure to set metadata
... Normally it gives some error message about why this failed. Is this on usegalaxy.org or another galaxy server? ...
written 2.2 years ago by Peter van Heusden150
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Comment: C: images for help section
... This is related to this issue: https://github.com/galaxyproject/galaxy/issues/1676 ...
written 2.2 years ago by Peter van Heusden150
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Comment: C: what is "your galaxy path" ????
... So with this all in your path, you then go sh /home/zsf/Downloads/executables/galaxy/run.sh ? I think, however, the subshell that Galaxy uses to run the tool does not inherit the path. You could try adding: PATH=$PATH:/home/zsf/Downloads/executables/annovar/:/home/zsf/Downloads/executables/gala ...
written 2.2 years ago by Peter van Heusden150
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Answer: A: images for help section
... Unfortunately the tool is going to be installed in a location that is not served by the Galaxy server, so what you describe wouldn't work. It is an interesting idea though, so perhaps an API could be added to the tools API (in lib/galaxy/webapps/galaxy/api/tools.py) that allowed tools to expose a im ...
written 2.2 years ago by Peter van Heusden150
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Answer: A: what is "your galaxy path" ????
... "Your galaxy path" in this case is the [PATH][1] environment variable available to your Galaxy server. So in your case, table_annovar.pl needs to be in a directory that is in PATH so that Galaxy can run it. So, at the point where you are doing the `sh /home/zsf/Downloads/executables/galaxy/run.sh`, ...
written 2.2 years ago by Peter van Heusden150
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Comment: C: Problem with bam files for exome sequencing analysis
... Hi Nadja I presume this data is on usegalaxy.org? If it is, could you please run the BAM files through the Flagstat tool and report on the statistics? And which species are these reads from? ...
written 2.2 years ago by Peter van Heusden150
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Answer: A: Cannot upload data from the local file
... If you see this behaviour on your Galaxy server (not usegalaxy.org): 1. You choose to upload files, and see the following page: ![Galaxy upload, Start not pressed][1] 2. You hit start but it never gets to a page like this, with the bar all Green and the message "Adding to history": ![Galaxy upl ...
written 2.2 years ago by Peter van Heusden150
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Comment: C: Galaxy toolshed information
... You need to setup your own server or launch one on a cloud (e.g. Amazon EC2 or Jetstream) using Cloudlaunch (https://usegalaxy.org/cloudlaunch). ...
written 2.2 years ago by Peter van Heusden150
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Comment: C: Galaxy toolshed information
... You are using Galaxy Main? As in usegalaxy.org? You (and I) are indeed not admins on this server, thus you cannot add tools to this server. ...
written 2.2 years ago by Peter van Heusden150

Latest awards to Peter van Heusden

Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: images for help section
Scholar 2.2 years ago, created an answer that has been accepted. For A: images for help section
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: images for help section

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