User: kramdi.a

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kramdi.a40
Reputation:
40
Status:
New User
Location:
France
Last seen:
1 year, 9 months ago
Joined:
4 years, 4 months ago
Email:
k*******@gmail.com

Posts by kramdi.a

<prev • 8 results • page 1 of 1 • next >
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Galaxy main .gitignore ignores *.sample files?
... Hi, I am testing the update process which is pretty straight-forward as mentioned [here][1]. So we basically git pull from Galaxy GitHub repo (from master branch), take a look at the new sample files just pulled and edit the corresponding config files if needed. The .gitignore file in the Galaxy ...
updates galaxy gitignore written 21 months ago by kramdi.a40 • updated 21 months ago by Martin Čech ♦♦ 4.8k
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Answer: A: Having trouble passing outputs through a wrapper
... I actually found what was wrong this morning, a silly inadvertence error when I copy the outputs. As you can see there are 5 shutil.move() calls when I only need to move 4 files (no more copy/paste..). Now the job completes successfully and I have access to all outputs in the history panel.  Howeve ...
written 4.4 years ago by kramdi.a40
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Having trouble passing outputs through a wrapper
... Hello,  I am trying to integrated a developed tool into Galaxy. I have to write a wrapper (I chose python) because the line command of my tool does not specify the outputs. -A few remarks: *I run a single user Galaxy instance (default install)  * my tool generates 4 outputs + 1 log file. You ca ...
wrapper python galaxy outputs written 4.4 years ago by kramdi.a40 • updated 3.4 years ago by rlee0350
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Comment: C: Single user Galaxy instance : job running for an unusually long time
... Hello, Thank you for your response. Yes, by basic install I mean the default "getgalaxy" distribution, it is suitable for development by a single user which is what I need. I am writing tool wrappers and I am only using Galaxy to test the tool's integration by running test with small datasets, I gue ...
written 4.4 years ago by kramdi.a40
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Single user Galaxy instance : job running for an unusually long time
... Hi,  I am testing a tool integration on my basic Galaxy instance. When I test the tool outside of Galaxy with relatively small set of data as inputs, it takes about 30min to complete. Now, after what I hope is a correct integrated into Galaxy (no errors), the job is running for several hours withou ...
galaxy yellow-state jobs written 4.4 years ago by kramdi.a40 • updated 4.4 years ago by Jennifer Hillman Jackson25k
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Comment: C: Galaxy wrapper for a tool that takes a configfile.txt
... You have been very helpful, thank you !   ...
written 4.4 years ago by kramdi.a40
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Comment: C: Galaxy wrapper for a tool that takes a configfile.txt
... Thank you for your quick and clear reply. I think my biggest problem is with Cheetah syntax , almost all example wrappers I studied use it, my head is burning with questions as I don't find the documentation very clear. If you could answer some of my basic questions, it would be very kind and helpfu ...
written 4.4 years ago by kramdi.a40 • updated 4.4 years ago by Martin Čech ♦♦ 4.8k
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Galaxy wrapper for a tool that takes a configfile.txt
... Hi, Maybe I'm asking a beginner question, please bear with me.  I'm currently in charge of the integration of a tool into Galaxy (I am doing it for the first time, with modest programming skills). My tool (coded in C++) takes input files AND a configuration file (configfile.txt) as arguments. It g ...
galaxy wrappers configfile arguments written 4.4 years ago by kramdi.a40 • updated 4.4 years ago by Dave B.410

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Popular Question 4.2 years ago, created a question with more than 1,000 views. For Galaxy wrapper for a tool that takes a configfile.txt

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