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This is the discussion forum, and Q&A section for Anduril Analysis Framework. For more information, head to www.anduril.org

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Alejandra Cervera2

11/3/17

So the error was that in a QuickBash instance I forgot to create the out output ....

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So the error was that in a QuickBash instance I forgot to create the out output ....

11/3/17

Anton Kulaga, Ville Rantanen4

1/16/17

Where are anduril artifacts published?

okay, thanks for the clarifications the jar files are stored there mostly for historical reasons, the

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scripting-syntax-and-usage

Where are anduril artifacts published?

okay, thanks for the clarifications the jar files are stored there mostly for historical reasons, the

1/16/17

Alexander Kanitz, … Ville Rantanen8

6/17/16

Anduril 1.x: Handline output filename prefixes

Thanks, good to know. Best, Alex

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Anduril 1.x: Handline output filename prefixes

Thanks, good to know. Best, Alex

6/17/16

Mikhail Pachkov, Ville Rantanen2

4/20/16

catching failures

Hi, One easy approach is to do this after anduril finishes. If a component fails, anduril exits with

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catching failures

Hi, One easy approach is to do this after anduril finishes. If a component fails, anduril exits with

4/20/16

Christian Frech, Ville Rantanen2

10/12/15

Reproducible bioinformatics pipelines with Docker and Anduril

brillant. thanks a bunch!

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scripting-syntax-and-usage

Reproducible bioinformatics pipelines with Docker and Anduril

brillant. thanks a bunch!

10/12/15

Christian Frech

8/19/15

Experiences with workflows for automating data-intensive bioinformatics

Maybe of interest for many in here: http://www.biologydirect.com/content/10/1/43 The CSC/Espoo is

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Experiences with workflows for automating data-intensive bioinformatics

Maybe of interest for many in here: http://www.biologydirect.com/content/10/1/43 The CSC/Espoo is

8/19/15

Christian Frech, Ville Rantanen5

6/10/15

Debian-based Anduril 1.2 docker image

I've now included the docker file to these images' descriptions: https://registry.hub.docker.

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component-issues

Debian-based Anduril 1.2 docker image

I've now included the docker file to these images' descriptions: https://registry.hub.docker.

6/10/15

Ikram Ullah, Ville Rantanen3

5/18/15

QCFasta: QCParser.pl can't find componentSkeleton.pm file

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component-issues

QCFasta: QCParser.pl can't find componentSkeleton.pm file

5/18/15

Ikram Ullah, Ville Rantanen3

5/18/15

Case folding collision while cloning microarray bundle

Thanks Ville! It works now.

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Case folding collision while cloning microarray bundle

Thanks Ville! It works now.

5/18/15

Christian Frech, … Ville Rantanen10

5/4/15

ArrayCombiner throws error in remote execution mode that _index file is missing

Good that you found this one out! if you want to appear 'smart', you can run this command in

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component-issues

ArrayCombiner throws error in remote execution mode that _index file is missing

Good that you found this one out! if you want to appear 'smart', you can run this command in

5/4/15

Christian Frech, Ville Rantanen9

4/29/15

Dockerizing Anduril components

There is an interesting related discussion going on over at reddit about interchangable

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Dockerizing Anduril components

There is an interesting related discussion going on over at reddit about interchangable

4/29/15

Alexander Kanitz, Ville Rantanen2

4/15/15

Optional output ports

Hi, and thanks for the interest! About the optional output ports, the current design (and Anduril2)

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component-issues

Optional output ports

Hi, and thanks for the interest! About the optional output ports, the current design (and Anduril2)

4/15/15

marko.k...@gmail.com, Ville Rantanen3

6/5/14

Non-ASCII characters in AndurilScript

What I would like to do is: authors = "Åke,Günter" \\ this should read "\u00C5ke,G\

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scripting-syntax-and-usage

Non-ASCII characters in AndurilScript

What I would like to do is: authors = "Åke,Günter" \\ this should read "\u00C5ke,G\

6/5/14

Foivos Gypas, lauri...@gmail.com5

4/23/14

remote execution problem

Hi guys Just to let you know, the problem was fixed. You just need to use "--exec-mode remote

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scripting-syntax-and-usage

remote execution problem

Hi guys Just to let you know, the problem was fixed. You just need to use "--exec-mode remote

4/23/14

Foivos Gypas, Ville Rantanen4

3/28/14

Clean output of specific components

There is a dirty trick that can achieve the effect, if needed right now. It's dirty, because in

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scripting-syntax-and-usage

Clean output of specific components

There is a dirty trick that can achieve the effect, if needed right now. It's dirty, because in

3/28/14

Foivos Gypas, … lauri...@gmail.com11

3/12/14

Anduril wrapper in version 1.2.22

Hello I just added the bundle to the component. Foivos

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component-issues

Anduril wrapper in version 1.2.22

Hello I just added the bundle to the component. Foivos

3/12/14

lauri...@gmail.com, Ville Rantanen4

2/14/14

Features lacking documentation in various places

Problem is I don't know (TM) or recall how the feature works, if there was something else to it,

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scripting-syntax-and-usage

Features lacking documentation in various places

Problem is I don't know (TM) or recall how the feature works, if there was something else to it,

2/14/14

lauri...@gmail.com

1/31/14

Generating a new component quick and dirty (python/bash)

Usually the task described here can be done with BashEvaluate or PythonEvaluate. However a component

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Generating a new component quick and dirty (python/bash)

Usually the task described here can be done with BashEvaluate or PythonEvaluate. However a component

1/31/14

marko.k...@gmail.com, Ville Rantanen2

12/13/13

Anduril2 repository versus anduril2 branch

The second repository has now been deleted, we have decided to branch the original. First commits in

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Anduril2 repository versus anduril2 branch

The second repository has now been deleted, we have decided to branch the original. First commits in

12/13/13

Marcin Cieślik, Ville Rantanen4

11/28/13

PBS/Torque and iteration

Thank you for the clear answers, the prefix scripts would be greatly appreciated (I think the could

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PBS/Torque and iteration

Thank you for the clear answers, the prefix scripts would be greatly appreciated (I think the could

11/28/13

lauri...@gmail.com

2/26/14

How to run a single step or component instance in a pipeline without disturbing the pipeline state

Background Normally if you vary inputs, parameters or outputs of a single component in Anduril, the

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How to run a single step or component instance in a pipeline without disturbing the pipeline state

Background Normally if you vary inputs, parameters or outputs of a single component in Anduril, the

2/26/14

Ville Rantanen, lauri...@gmail.com2

10/2/13

Iterating arrays and @keep=false

In the iter branch there is an alternate syntax. It's probably going to incorporated into Anduril

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scripting-syntax-and-usage

Iterating arrays and @keep=false

In the iter branch there is an alternate syntax. It's probably going to incorporated into Anduril

10/2/13

9/11/13

How to download large filesets.

Since Anduril is designed to re-execute the incomplete and failing processes, it may be tedious to

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How to download large filesets.

Since Anduril is designed to re-execute the incomplete and failing processes, it may be tedious to

9/11/13

lauri...@gmail.com, Ville Rantanen3

9/11/13

Producing a CSV file with multiple columns, each referring to Anduril ports

Can't you simply use the arrays? Or is the CSV for some specific input (where the component needs

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component-issues

Producing a CSV file with multiple columns, each referring to Anduril ports

Can't you simply use the arrays? Or is the CSV for some specific input (where the component needs

9/11/13

lauri...@gmail.com

9/12/13

Inputting multiple lines in strings and creating text files in your scripts

If you know how to use strings enclosed in single or double quotes, such as 'foo' and "

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scripting-syntax-and-usage

Inputting multiple lines in strings and creating text files in your scripts

If you know how to use strings enclosed in single or double quotes, such as 'foo' and "

9/12/13

lolmo, … Ville Rantanen3

8/23/13

How do I access multiple files from a folder in anduril?

I can present a piece of code explaining the action my_folder=INPUT(path="path_to_folder")

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scripting-syntax-and-usage

How do I access multiple files from a folder in anduril?

I can present a piece of code explaining the action my_folder=INPUT(path="path_to_folder")

8/23/13

lauri...@gmail.com, Ville Rantanen3

8/14/13

How to print the file names of all the input ports in an array

okay, so let's solve this from the beginning, for key, file: array { This syntax refers to

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scripting-syntax-and-usage

How to print the file names of all the input ports in an array

okay, so let's solve this from the beginning, for key, file: array { This syntax refers to

8/14/13

Ville Rantanen2

8/9/13

Generate a column of random numbers

Note, that while this example does not now use an input, it is presented here because sometimes you

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Generate a column of random numbers

Note, that while this example does not now use an input, it is presented here because sometimes you

8/9/13

8/9/13

Transpose a 2D record

Ever had to iterate and collect data from a component that produces several outputs? You might have

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scripting-syntax-and-usage

Transpose a 2D record

Ever had to iterate and collect data from a component that produces several outputs? You might have

8/9/13

Ville Rantanen2

7/4/13

java.lang.NoClassDefFoundError: fi/helsinki/ltdk/csbl/asser/pipeline/SearchReplaceComponent

you are missing the microarray.jar in the microarray bundle lib/java build it by going to the

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component-issues

java.lang.NoClassDefFoundError: fi/helsinki/ltdk/csbl/asser/pipeline/SearchReplaceComponent

you are missing the microarray.jar in the microarray bundle lib/java build it by going to the

7/4/13

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