Andrew Davidson
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Recent activity by Andrew Davidson
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output directory is missing? /cromwell_root/script: line 103: 22 Killed salmon quant
I wrote a workflow that uses Salmon. One of the arguments to salmon is --output, ie the directory salmon will write to. Before calling salmon I call ```mkdir salmon.out``` salmon runs for about 10 ...
- 2 followers
- 16 comments
- 0 votes
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trick to make bash tasks easier to debug
FYI Here is a trick so that you can use `set -x`. to create bash script trace of the execution. this can be handy for debugging. You will see the command and the output in a single file. enjoy, s...
- 1 follower
- 0 comments
- 1 vote
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'task command' how to work with local variables
I having trouble writing tasks. I think the issue is that you can not simply cut and past bash scripts. This like variable substitution do not work as expected. I wonder if there is some more detai...
- 3 followers
- 3 comments
- 0 votes
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how can I find my "job cost" is
Hi I am working on a proof of concept for my Lab. One of the things I need to do is estimate the cost for a very large workflow. My plan was to run the workflow on a small set of sample and use th...
- 2 followers
- 1 comment
- 0 votes
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RFE: making it easier to work with files and workflow execution buckets
I am working through a proof of concept project for my lab. I am very impressed with Terra so far. I understand the need to name buckets using GUIDs however it is not very human-friendly. Bellow, ...
- 2 followers
- 2 comments
- 1 vote
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it hard to add new tasks to an existing name space
I am a newbie. I want to use the namespace like a package in java. that is to say I have several tasks in the same name space when I create a new task it would be much less error prone if there was...
- 2 followers
- 4 comments
- 0 votes