User: Stef van Lieshout

Reputation:
10
Status:
New User
Location:
Netherlands
Last seen:
2 years, 4 months ago
Joined:
3 years, 7 months ago
Email:
s**************@fastmail.fm

Posts by Stef van Lieshout

<prev • 8 results • page 1 of 1 • next >
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Answer: A: bwa mem index builder error
... I see now I get the exact same error with the SNPeff data manager.... ValueError: dictionary update sequence element #0 has length 6; 2 is required ...
written 2.4 years ago by Stef van Lieshout10
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Answer: A: bwa mem index builder error
... Nobody an idea what goes wrong here? Dan, do you remember what the problem mentioned in the trello card was? ...
written 2.4 years ago by Stef van Lieshout10
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Answer: A: bwa mem index builder error
... Maybe it has to do with the following trello card: https://trello.com/c/MZGPlWuk/2098-pull-request-510-fix-for-data-manager-failure-to-update-a-dict-when-a-list-is-passed-instead-of-a-dict It has the exact same ValueError named and you archived it Dan, saying "PR was declined, as error wasn't due t ...
written 2.4 years ago by Stef van Lieshout10
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Answer: A: bwa mem index builder error
... Ok, yes there is info there, although I dont know what is meant with the "dictionary update sequence" mentioned? Traceback (most recent call last): File "/mnt/data/galaxy-home/tst-ctmm-gal/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 378, in finish_job remote_working_directory=remote_wo ...
written 2.4 years ago by Stef van Lieshout10
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bwa mem index builder error
... I would like to use the BWA mapper tool so I installed the tool "bwa" from "devteam" from main toolshed in our local galaxy: https://toolshed.g2.bx.psu.edu/view/devteam/bwa/ac30bfd3e2a8 To get the genome index I installed "data_manager_bwa_mem_index_builder": https://toolshed.g2.bx.psu.edu/view/dev ...
index builder bwa bwa-mem written 2.4 years ago by Stef van Lieshout10
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Information about new galaxy releases / changes?
... I know there is issue tracking...but is there also a page with an overview of (major) changes or new features in upcoming galaxy releases? And perhaps a planning for release dates? ...
release galaxy written 3.5 years ago by Stef van Lieshout10 • updated 3.5 years ago by Greg Von Kuster810
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Answer: A: using R data structure files (rds) as input/output in galaxy tools
... Hi Bjoern, I tried adding the datatype to datatypes_conf.xml but was missing "type", "minetype" and "subclass", which were apparently required... With your suggestion it works perfectly, many thanks! ...
written 3.6 years ago by Stef van Lieshout10
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using R data structure files (rds) as input/output in galaxy tools
... So I've been able to create a tool wrapper for an R script and make it work in my local Galaxy instance. Next step is to ouput an R data structure (rds) file from this tool and implement a next R script that uses this rds file as input. While the outputting (to history) seems to work, using rds agai ...
R datatypes galaxy written 3.6 years ago by Stef van Lieshout10

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