User: David Managadze

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United States
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3 years, 1 month ago
Joined:
4 years ago
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d*********@gmail.com

Computational biologist interested in genomics, big data, and large pipelines. Loves Python. Works at NCBI

Posts by David Managadze

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Integrate pipeline (set of custom tools) into Galaxy
... Frederik, I made some progress passing a directory path to the next app. See https://biostar.usegalaxy.org/p/13641 There is an unsolved problem too in that post. I would really appreciate if you could give me some hints about 'from_work_dir' if you made them work. Thanks.   ...
written 3.1 years ago by David Managadze10
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Answer: A: Integrate pipeline chain of apps with multiple output files
... I fixed my problem but partially. In the first app's XML, I set output like this: <outputs> <data name="output" format="hg_mft" from_work_dir="out/trees.mft" label="FastTree Mft"/> </outputs> Here, "./out/trees.mft" is a "Manifest" file the first app's work directory. I came ...
written 3.1 years ago by David Managadze10
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Answer: A: Integrate pipeline (set of custom tools) into Galaxy
... Thanks Martin! RE: Can the set of your apps be approached as a one Galaxy Tool?  I am not sure. Some of them can be used in different contexts, and the reason that I am trying to integrate them into Galaxy is that I might want to connect them in different ways. I thought about something like this: ...
written 3.1 years ago by David Managadze10
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Comment: C: Integrate pipeline (set of custom tools) into Galaxy
... The question about multiple files you are referring to is opened by me and there is no answer yet. Also, this post is not just about multiple files. This is about general architecture and a way of integrating a separate, existing pipeline into Galaxy. What I'd like to know is how to keep the state ...
written 3.1 years ago by David Managadze10
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Integrate pipeline (set of custom tools) into Galaxy
... I have created a set of apps for running a pipeline. The individual apps can be started from the command line and they have unified interface and parameters. For instance all of them have parameters: --input # to tell that the input is a directory --workdir # working directory where the app mu ...
custom tool pipeline galaxy integration written 3.1 years ago by David Managadze10 • updated 3.1 years ago by frederik.coppens40
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Integrate pipeline chain of apps with multiple output files
... I wrote a pipeline, a set of apps in Python. Every app outputs thousands of files. Every app will create a main work directory (aka $app_workdir, path provided in command line) and put all the final output data in $app_workdir/out/, all the logs in $app_workdir/log/, all temporaries in $app_workdir/ ...
custom tool output multiple files written 3.1 years ago by David Managadze10

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