User: marcoalbuquerque.sfu

Reputation:
50
Status:
New User
Location:
Canada
Last seen:
1 year, 3 months ago
Joined:
3 years, 1 month ago
Email:
m*******************@gmail.com

Posts by marcoalbuquerque.sfu

<prev • 29 results • page 1 of 3 • next >
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Adding a toolshed to .planemo.yml that isn't local, the testtoolshed and or main toolshed
... I was wondering if there is a way to add a shed_target to .planemo.yml that is a none of the current three shed targets the file is initialised with. Essentially we have a local toolshed hosted on a virtual machine, but several users are developing on different machines and thus the toolshed is not ...
shed_upload shed_target toolshed planemo written 16 months ago by marcoalbuquerque.sfu50 • updated 16 months ago by Martin Čech ♦♦ 4.3k
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Comment: C: Dynamic Options Not Filling In
... This seems inconvenient. So you need to run a tool prior that fetches this data before running the actual tool? Would be nice if it was handled internally. Is there a way to run a pre-command and generate a dataset of options before submitting a tool? ...
written 17 months ago by marcoalbuquerque.sfu50
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Dynamic Options Not Filling In
... I am trying to use dynamic options in galaxy but it isn't working. Essentially a user can include a covariate tabular file. In this file there will be columns which could be added to a multi plot figure script we are working on to summarize SNVs across a cohort. Here is an example tool config file ...
dynamic_options galaxy written 18 months ago by marcoalbuquerque.sfu50 • updated 17 months ago by Hotz, Hans-Rudolf1.7k
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Storing Environment Variables for Predefined Environment Variables
... I am trying to create an environment variable of which will be stored in env.sh for an environment variable that already exists. Essentially I am fetching predefined JAVA environment variables using the following: R CMD javareconf -e This command defines a series of environment variables, som ...
rjava environment galaxy written 18 months ago by marcoalbuquerque.sfu50
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Answer: A: Fetching Time Statistics from Galaxy Database
... I think I have figured this out. The table : model.JobMetricNumeric.table I grepped "time" in all python files present in galaxy/lib/job I found a tool (rule_helper.py) which uses this metric runtime_seconds from the table listed above. I queried this table, and noticed there were a few other me ...
written 2.3 years ago by marcoalbuquerque.sfu50
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Fetching Time Statistics from Galaxy Database
... Hello BioStars, I am trying to get some runtime statistics from some jobs I have submitted on a local instance of galaxy. Essentially I want the Job Start Time and the Job End Time as listed on each job information pane.  I have investigated the database using the tutorial from the GCC2015. I also ...
time database galaxy schema written 2.3 years ago by marcoalbuquerque.sfu50 • updated 2.3 years ago by Jennifer Hillman Jackson24k
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Comment: C: Making Changes to Data Tables in Tools
... This is exactly what I wanted! Thanks so much. ...
written 2.5 years ago by marcoalbuquerque.sfu50
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Comment: C: Making Changes to Data Tables in Tools
... If it helps, here is a further explanation of exactly what I am trying to do. From what I know, data tables require manual setup before being able to use them. It would be really cool if there were ways to add new data entries to the table, automatically, within tools. Why? Some references are more ...
written 2.5 years ago by marcoalbuquerque.sfu50
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Making Changes to Data Tables in Tools
... Lets say I wanted to have a tool that would install a genome and annotation information. And lets say that this tool automatically added entries to the packages data table. Would this data table need to be reloaded? In other words, would the galaxy instance need to be rebooted for the user to run o ...
data tables tools annotation genome written 2.5 years ago by marcoalbuquerque.sfu50 • updated 2.5 years ago by Jennifer Hillman Jackson24k
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Parallelism with Multiple Outputs : HOW?
... First Question, Where in the Galaxy file system are the parallelism modules defined? I.e. where can if learn how galaxy handles parallelism? Second - Real - Question, Given the following tag: <parallelism method="multi" split_inputs="interval_file" split_mode="to_size" split_size="1" shared_ ...
tag galaxy parallelism written 2.9 years ago by marcoalbuquerque.sfu50 • updated 2.9 years ago by Jennifer Hillman Jackson24k

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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Automatic BAM Index creation but tool is unsuccessful in identifying index
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Need help setting up a virtual environment to write a python wrapper from tool s

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