Dear all,
I wanted to know if the tool prinseq will be available in the main toolshed, because I saw that the wrapper and tool dependency are already available here in the github https://github.com/bgruening/galaxytools/tree/master/tools/prinseq ?
Thanks,
Hello,
The tool is wrapped in the Test Tool Shed by the same auther (Bjoern Gruening).
http://testtoolshed.g2.bx.psu.edu/
Best, Jen, Galaxy team
Hello,
thanks for your email indeed it is available in the testtoolshed but when I am trying to find it via my Galaxy by clicking on Galaxy tool shed I can't find it.
And i checked my shed_tool xml file has the good links :
<?xml version="1.0"?>
<tool_sheds>
<tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/>
<tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/>
</tool_sheds>
Any idea or another link ?
Thanks
Hi, Also check your ../contig/galaxy.ini file, this block:
# Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). #tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
The last line should be uncommented and probably both conf files created (since the tool_conf.xml.sample won't be used anymore). I believe that you need to restart the server after any config changes.
Let us know if this helps or not, Jen, Galaxy team
Hello Jennifer,
Thanks for your message.
Unfortunately it does not work.
So here some paths in the galaxy.ini :
# Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). tool_config_file = /home/galaxy/galaxy-dist/config/tool_conf.xml,/home/galaxy/galaxy-dist/config/shed_tool_conf.xml
Then the tool_sheds_conf.xml :
# File containing the Galaxy Tool Sheds that should be made available to # install from in the admin interface (.sample used if default does not exist). tool_sheds_config_file = /home/galaxy/galaxy-dist/config/tool_sheds_conf.xml
I checked the tool_sheds_conf.xml :
<?xml version="1.0"?>
<tool_sheds>
<tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/>
<tool_shed name="Galaxy test tool shed" url="https://testtoolshed.g2.bx.psu.edu/"/>
</tool_sheds>
But I don't have the option of prinseq when i am clicking in test tool shed via admin and i saw it in the testtoolshed link :
my test toolsheds https://www.dropbox.com/s/7dirpq9rpm6ak9h/my_testtoolsheds.png?dl=0
main test toolsheds https://www.dropbox.com/s/spzrc570vxmv2g9/testtoolsheds.PNG?dl=0
Thanks in advance,
Dear all,
I tried to install prinSeq via the the testtoolshed of my Galaxy instance but I coul not find it, finally I tried to install it by myself.
So I downloaded the tool from https://testtoolshed.g2.bx.psu.edu/ hg clone https://testtoolshed.g2.bx.psu.edu/repos/bgruening/prinseq.
Then I changed in tool_shed.xml the path to the prinseq.xml and also in the prinseq.xml I cnaged the path to bin of prinseq tools.
First thing, there was a problem to read the prinseq.xml by Galaxy because there was missing a tag </inputs>.
Then when I wanted to use the tool and execute the job, I have a blank page.
And the code error is
galaxy.tools ERROR 2015-03-24 21:07:32,366 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1130, in handle_single_execution job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1694, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 270, in execute handle_output( name, output ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 247, in handle_output data.init_meta( copy_from=inp_data[output.metadata_source] ) KeyError: 'seq_type.input_singles'
If someone can help because I don't understand this error.
Thanks in advance...
