On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt <m.bernt@ufz.de> wrote:
Dear galaxy-dev list,
I'm currently trying to introduce myself to the galaxy server, i.e., learning how to use and administer a galaxy server.
I have installed galaxy following this excellent tutorial:
https://github.com/martenson/dagobah-training
Then I tried the tool "FASTQ Quality Trimmer by sliding window" which is mentioned in NGS101-6 tutorial. I installed the tool from tool shed, but I get a python error (the Admin panel shows that all dependencies are installed):
Traceback (most recent call last): File "/home/berntm/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py", line 3, in <module> from galaxy_utils.sequence.fastq import fastqReader, fastqWriter File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, in <module> from six import Iterator, string_types ImportError: No module named six
Do you have an idea what could be wrong? I guess that this is to little information, but I did not know which kind of additional information would be helpful.
This appears to be a missing dependency on the Python module "six" which is used to help write code which will work under both Python 2 and Python 3. This is likely a recent regression - hopefully one of the Galaxy team can comment on this, likely the Tool Shed definition for this tool needs a minor tweak (and then you can apply the update via the Galaxy Admin controls within your browser).
Another question: At my institution quite a lot of NGS projects are carried out. After a project is finished all methods and data are stored to a long term read only tape archive. For the future the idea is to use galaxy. Which options are there to implement such a project life cycle with galaxy?
Not that I personally am aware of, no. There are optional disk quotas to encourage users to remove (delete) old data.
A last general question: would it be better to send a separate mail to the list when I have multiple questions?
Yes please, with useful email subjects would be best. Peter