Question: PRINSEQ toolshed ?
0
gravatar for k.mamoud
3.7 years ago by
k.mamoud30
Switzerland
k.mamoud30 wrote:

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,

 

 

prinseq toolshed tool galaxy • 1.0k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by k.mamoud30
1
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

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

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k

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

 

ADD REPLYlink written 3.7 years ago by k.mamoud30

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

ADD REPLYlink written 3.7 years ago by Jennifer Hillman Jackson25k

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,

 

 
ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by k.mamoud30

Hello, Just type in the tool name into the search box, not by going through "Search for valid tools" first. Thanks, Jen, Galaxy team

ADD REPLYlink written 3.7 years ago by Jennifer Hillman Jackson25k

Hello Jennifer,

thanks for your message.

So I tried to install it by clicking on Galaxy test tool shed button then I put prinseq on the saerch box but nothing No items ...

 

Thanks,

 

ADD REPLYlink written 3.7 years ago by k.mamoud30
0
gravatar for k.mamoud
3.7 years ago by
k.mamoud30
Switzerland
k.mamoud30 wrote:

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...

 

 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by k.mamoud30
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