Re: [galaxy-dev] ImportError and Project life cycle
Hi Matthias, to your life cycle question, do you have more information about your filesystem(s) and what you have specifically in mind? Everything is possible I guess, from a hack to a advanced solution like iRODS. My feeling is that this should be implemented on the FS level and not on the Galaxy level. Ciao, Bjoern > 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 > from galaxy_utils.sequence.fastq import fastqReader, fastqWriter > File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, > in > 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. > > 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? > > A last general question: would it be better to send a separate mail to > the list when I have multiple questions? > > Best regards, > Matthias Bernt > > > ___ > 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/ ___ 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/
Re: [galaxy-dev] ImportError and Project life cycle
Hi Matthias, what version of Galaxy are you running? The tool you have installed seems to support only new Galaxies that have Conda dependency resolution enabled. We are currently in the middle of the transition of the Galaxy's ecosystem to this new dependency manager so there are rough edges here and there - sorry about that. You can read details about Conda and dependency resolution here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html Since Galaxy 16.07 you can switch the `conda_auto_init` in Galaxy's config to True and after restart Galaxy will install Conda itself. Therefore I recommend you (with Galaxy newer than 16.07) to uninstall the tool, install Conda (with conda_auto_init) and install the tool again. That will install the needed dependency for the tool. If you have older Galaxy please update it. Please let us know about any questions you have and thanks for using Galaxy. Martin On Fri, Feb 10, 2017 at 10:38 AM Peter Cock wrote: > On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt 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 > > from galaxy_utils.sequence.fastq import fastqReader, fastqWriter > > File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, > in > > > > 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/ ___ 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/
Re: [galaxy-dev] ImportError and Project life cycle
On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt 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 > from galaxy_utils.sequence.fastq import fastqReader, fastqWriter > File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, in > > 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/
[galaxy-dev] ImportError and Project life cycle
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 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, in 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. 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? A last general question: would it be better to send a separate mail to the list when I have multiple questions? Best regards, Matthias Bernt ___ 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/
