User: e.rempel

gravatar for e.rempel
e.rempel30
Reputation:
30
Status:
New User
Location:
Germany
Last seen:
1 month, 3 weeks ago
Joined:
3 years, 1 month ago
Email:
e*******@dkfz-heidelberg.de

Posts by e.rempel

<prev • 8 results • page 1 of 1 • next >
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High load average on local Galaxy Instance
... Hello everybody, lately we are experiencing some problems with our local Galaxy instance: [Very slow start-up][1] and very high load average caused by Galaxy: have a look at [htop output][2]. Is it normal that so many `paster.py server` processes are running in parallel? It looks to me as if multip ...
galaxy software error written 8 weeks ago by e.rempel30 • updated 8 weeks ago by Jennifer Hillman Jackson25k
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Comment: C: Very slow start up of local Galaxy instance
... Hi Jen, thank you for your response. Actually, we are still using the 17.01 version. We are going to update it in next months. Hopefully, this issue would go away. In the meantime, if there is something we can try to remedy, please, let me know. Best, Eugen ...
written 8 weeks ago by e.rempel30
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Very slow start up of local Galaxy instance
... Hi all, yesterday I have encountered a problem of a very slow (several minutes) start-up of a local Galaxy instance. Using tail -f paster.log I saw some kind of a loop: lines were reappearing over and over again. The output of tail -f paster.log | grep 'Adding an entry for version 0.7.1 ...
galaxy software error written 8 weeks ago by e.rempel30 • updated 8 weeks ago by Jennifer Hillman Jackson25k
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Answer: A: Error installing Biopython 1.67
... Thank you, Jen. At the end, we used the suggestion in [Fix PyPI URL for biopython-1.67.tar.gz][1] and it worked. [1]: https://github.com/biopython/galaxy_packages/commit/581b206359f1f59f60b61f749dd3f7b6d6f045f7 ...
written 14 months ago by e.rempel30
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Error installing Biopython 1.67
... Dear Galaxy community, we experience difficulties with installing Biopython package (version 1.67). The error message is: Error downloading from URL https://pypi.python.org/packages/source/b/biopython/biopython-1.67.tar.gz : HTTP Error 404: Not Found It looks like the link https://pypi.python.or ...
dependency biopython written 14 months ago by e.rempel30
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Answer: A: Orphan dataset after Exporting history to file
... There is a simple solution to this problem (pointed out by Bjoern Gruening, thanks!): pgcleanup.py - A script for cleaning up datasets in Galaxy efficiently, by bypassing the Galaxy model and operating directly on the database (https://github.com/galaxyproject/galaxy/blob/dev/scripts/cleanup_dataset ...
written 14 months ago by e.rempel30
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Orphan dataset after Exporting history to file
... Dear all, we are running a local Galaxy (an older release) instance and encounter the following issue. After exporting history to file there is an "orphan" dataset left (in galaxy/database/files/...). It looks like it doesn`t belong to any history, thus the cleanup scripts cannot delete it. Of cour ...
export history written 14 months ago by e.rempel30
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Answer: A: Galaxy installation on ubunto failed while running run.sh
... I had a similar error message running a python script. I fixed it by installing python module "bx-python" via "pip" as follows pip install bx-python Be sure that you have the package "numpy" previously installed. Regards, Eugen Rempel     ...
written 2.3 years ago by e.rempel30

Latest awards to e.rempel

Scholar 14 months ago, created an answer that has been accepted. For A: Error installing Biopython 1.67

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