On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt <m.be...@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/