Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01
I guess this relates directly to my question as well... On 03/03/2016 01:06 PM, Makis Ladoukakis wrote: Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis ___ 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/ -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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] trouble with python packages after galaxy update
Hi Guys, So i updated my galaxy instance to release_16.01 I usually started galaxy in a venv and used pip to install any packages my tool needed. (in this case, numpy and scipy) source my_galaxy_dir/.venv/bin/activate pip install scipy (dependency numpy also installed) ./run.sh But since the last update, i am having problems with this. Did something change? because it looks like it searches for an existing venv and then activates a new venv in my already active one?? Depending on what i try, when i execute my tool in galaxy, my messages range from ImportError: No module named scipy or ValueError: numpy.dtype has the wrong size, try recompiling <http://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling> I tried running galaxy without a venv, re-creating my venv. renaming my venv installing numpy, then scipy, not using pip at all. removing numpy and reinstalling without cache. I also played around with pip, doing nothing after creating my venv, or first upgrading my pip, but then after i start galaxy i get this message: (.venv)@server:/galaxy-dist$ ./run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple Collecting pip==8.0.2+gx2 Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB) 100% || 1.2MB 339kB/s Installing collected packages: pip Found existing installation: pip 8.0.3 Uninstalling pip-8.0.3: Successfully uninstalled pip-8.0.3 Successfully installed pip-8.0.2+gx2 And later on i get the message that i should upgrade my pip... I am confused...can someone tell me the correct way to start galalxy within or without my venv and how to correctly install my packages? Thanks! with regards, Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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] parse history file/uploaded file with dynamic_options script
Hi Greg, Wow that was easy! I was not expecting that. Thank you! Linda On 09/22/2015 03:41 PM, Von Kuster, Greg wrote: Hi Linda, I think your parameter definition will need to send the file_name of the HistoryDatasetAssociation, something like this... In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section. My problem seems to be the following. In python, amplitudes is a galaxy object: How do I parse/access this file to get the headers? It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html Thanks! Linda -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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/ -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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] parse history file/uploaded file with dynamic_options script
Hi All, I am a bit lost here. In my xml I have the following sections: label="amplitude file"/> display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes)'/> In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section. My problem seems to be the following. In python, amplitudes is a galaxy object: How do I parse/access this file to get the headers? It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html Thanks! Linda -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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] dynamic_options within repeat or conditional block
Hi All, I am relatively new to galaxy and recently had to take over the work on several tools. After the last galaxy update, one of them stopped working. Old working code: repeat name=pref title=Select column name preference param name=columntype type=select label=Column name refresh_on_change=true dynamic_options='filter_column2(library_file, col_type, polarity)' / /repeat This worked perfectly, but now, the select shows me no options available When i move the param-tag out of the repeat block, it works again. Also, when i put this param within a conditional like: conditional name=col_pref param name=apply_select type=boolean checked=false label=Select column name preference? / when value=true param name=columntype type=select label=Column name refresh_on_change=true dynamic_options='filter_column2(library_file,col_type,polarity)'/ /when when value=false param name=model type=hidden value=False / /when /conditional the dynamic_options also does not work. I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-work-in-repeats This seems to be my problem too. Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround. Thank you, Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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] dynamic_options within repeat or conditional block
Thanks for your reply, I updated my instance and indeed it was fixed! I will update more frequently! Linda On 04/30/2015 03:29 PM, Aysam Guerler wrote: Hey Linda, This seems to be an issue which has already been fixed. Could you please update your instance and/or let me know at which commit it is? Thank you, Aysam On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker linda.bak...@wur.nl mailto:linda.bak...@wur.nl wrote: Hi All, I am relatively new to galaxy and recently had to take over the work on several tools. After the last galaxy update, one of them stopped working. Old working code: repeat name=pref title=Select column name preference param name=columntype type=select label=Column name refresh_on_change=true dynamic_options='filter_column2(library_file, col_type, polarity)' / /repeat This worked perfectly, but now, the select shows me no options available When i move the param-tag out of the repeat block, it works again. Also, when i put this param within a conditional like: conditional name=col_pref param name=apply_select type=boolean checked=false label=Select column name preference? / when value=true param name=columntype type=select label=Column name refresh_on_change=true dynamic_options='filter_column2(library_file,col_type,polarity)'/ /when when value=false param name=model type=hidden value=False / /when /conditional the dynamic_options also does not work. I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-work-in-repeats This seems to be my problem too. Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround. Thank you, Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 tel:%2B31-317-480756 email: linda.bak...@wur.nl mailto:linda.bak...@wur.nl ___ 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/ -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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/
