User: lindfors.erno

gravatar for lindfors.erno
Reputation:
30
Status:
New User
Location:
Germany
Last seen:
2 years, 2 months ago
Joined:
3 years, 7 months ago
Email:
l************@gmail.com

Posts by lindfors.erno

<prev • 11 results • page 1 of 2 • next >
1
vote
1
answer
702
views
1
answer
Bioblend - Accessing a content of Galaxy output without opening a web browser ?
... Hi all, Is there a way to access a content of Galaxy's output file without opening a web browser? I have implemented a simple test on Galaxy server that just writes a string to an output file. I have the following configuration file. <tool id="ReadOutputTest_R" name="ReadOutputTest" version="1.1 ...
galaxy bioblend written 2.3 years ago by lindfors.erno30 • updated 2.3 years ago by Martin Čech ♦♦ 4.6k
0
votes
0
answers
579
views
0
answers
Comment: C: Bioblend - Getting all parameters for a Galaxy tool ?
... Recently managed to google a solution:     for tool in tools:       toolShow = toolClient.show_tool(tool_id=tool['id'], io_details=True)       inputParams = toolShow['inputs'] ...
written 2.3 years ago by lindfors.erno30
1
vote
0
answers
579
views
0
answers
Bioblend - Getting all parameters for a Galaxy tool ?
... Hi all, I would like to get all parameters that a Galaxy tool has. More specifically, I have managed to get all tool panels and tools by using the following code snippet. import sys from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.tools import ToolClient galaxyInstance = GalaxyInsta ...
galaxy bioblend written 2.3 years ago by lindfors.erno30
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Bioblend - Passing a non-datasets parameter in toolClient.run_tool ?
... Yes the cond|choice indeed solved this, more specifically the follow parameter setting works: params = {'cond|choice': 'yes', 'cond|test_file':{'src': 'hda', 'id': testFile['outputs'][0]['id']}} Thanks very much for the help! ...
written 3.1 years ago by lindfors.erno30
2
votes
1
answer
1.4k
views
1
answer
Bioblend - Passing a non-datasets parameter in toolClient.run_tool ?
... Hi all, I am trying to pass a non-dataset parameter in toolClient.run_tool. More specifically, I am running the following code. from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.histories import HistoryClient from bioblend.galaxy.tools import ToolClient from bioblend.galaxy.datasets ...
galaxy software error bioblend written 3.5 years ago by lindfors.erno30
0
votes
1
answer
1.5k
views
1
answers
Comment: C: Bioblend - toolClient.run_tool does not work with more than one params ?
... Thanks, this solved the problem! And yes, they are just data parameters at the top level of the tool. With best regards, Erno Lindfors ...
written 3.5 years ago by lindfors.erno30
3
votes
1
answer
1.5k
views
1
answer
Bioblend - toolClient.run_tool does not work with more than one params ?
... Hi all, My purpose is to run a Galaxy tool with two parameters from command line via BioBlend. More specifically I am running the following code: from bioblend.galaxy import GalaxyInstance from bioblend.galaxy.histories import HistoryClient from bioblend.galaxy.tools import ToolClient from bioble ...
galaxy software error bioblend written 3.6 years ago by lindfors.erno30 • updated 3.5 years ago by jmchilton1.1k
0
votes
2
answers
767
views
2
answers
Answer: A: blend4j - Running a galaxy tool ?
... Thanks again for your prompt help! I have been looking into your improved blend4j package. However as you anticipated I feel maybe it is a bit too unstable for my purpose, so I think for the moment I will just call python directly from Java (a bit dirty but should work), and perhaps will switch to b ...
written 3.6 years ago by lindfors.erno30
4
votes
2
answers
767
views
2
answers
blend4j - Running a galaxy tool ?
... Hi all, How can I run a galaxy tool by using the blend4j package (http://jmchilton.github.io/blend4j/apidocs/) ? I have successfully managed to do it from Python command line (http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html) by using the following command: toolClient.run_tool(hi ...
galaxy blend4j written 3.6 years ago by lindfors.erno30
0
votes
2
answers
1.2k
views
2
answers
Answer: A: Question: Bioblend - upload_file does not work from command line ?
... Thanks for the reponse! I checked the dataset is indeed created in the history. ...
written 3.6 years ago by lindfors.erno30

Latest awards to lindfors.erno

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 102 users visited in the last hour