ruffus_discuss

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Welcome to the discussion group for the Ruffus python pipeline. Ruffus is a widely used (especially in bioinformatics) python library for lightweight computational pipelines.

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archana bhardwaj

9/23/19

error running simple ruffus code in windows

Hi I am trying to run very simple code of ruffus as demo from ruffus import * import sys def

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error running simple ruffus code in windows

Hi I am trying to run very simple code of ruffus as demo from ruffus import * import sys def

9/23/19

7/9/18

Ruffus spend a long time in thread lock

Hi, I am working on a ruffus bioinformatic pipeline that is intended to run several different

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Ruffus spend a long time in thread lock

Hi, I am working on a ruffus bioinformatic pipeline that is intended to run several different

7/9/18

Itai Rusinek, Clare Sloggett2

6/6/18

Removing intermediate (temp) files

Hi Itai, We dealt with this by "zeroing out" the intermediate files, ie overwriting them

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Removing intermediate (temp) files

Hi Itai, We dealt with this by "zeroing out" the intermediate files, ie overwriting them

6/6/18

Valentin Krasontovitsch

1/15/18

alternative to ruffus (in golang)

Hello everybody, even though it may be cheeky to pose this question here, I am currently looking for

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alternative to ruffus (in golang)

Hello everybody, even though it may be cheeky to pose this question here, I am currently looking for

1/15/18

Collioure, Valentin Krasontovitsch2

1/15/18

Issues with naming in Ruffus

Hi there, I think based on the pinned posts and recent activity it is quite safe to say that the

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Issues with naming in Ruffus

Hi there, I think based on the pinned posts and recent activity it is quite safe to say that the

1/15/18

archana bhardwaj2

8/25/17

ruffus test script not running

Its solved. Now I can work on ruffus easily. On Friday, August 25, 2017 at 2:29:44 PM UTC+5:30,

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ruffus test script not running

Its solved. Now I can work on ruffus easily. On Friday, August 25, 2017 at 2:29:44 PM UTC+5:30,

8/25/17

8/24/17

Fix for "disk I/O error" or running without SQLite

Hi, I am trying to use Ruffus 2.6.3 on a system where SQLite might not be installed correctly and

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Fix for "disk I/O error" or running without SQLite

Hi, I am trying to use Ruffus 2.6.3 on a system where SQLite might not be installed correctly and

8/24/17

Rad, … Valentin Krasontovitsch3

7/6/17

Ruffus and Testing

Dear Leo, I am also interested in writing some tests for a pipeline written with ruffus. At the first

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Ruffus and Testing

Dear Leo, I am also interested in writing some tests for a pipeline written with ruffus. At the first

7/6/17

Daniel, … Mark Schultz6

2/20/17

multiprocessing error

This worked for me too! I had a feeling that having everything inside a main() function was causing

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multiprocessing error

This worked for me too! I had a feeling that having everything inside a main() function was causing

2/20/17

1/30/17

Ruffus tag on stackoverflow

As I have noticed questions sometimes go unanswered on this google group I've created a tag on

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Ruffus tag on stackoverflow

As I have noticed questions sometimes go unanswered on this google group I've created a tag on

1/30/17

1/22/17

string too long to generate flowchart

I guyess my question should be, how do I stop rendering of the 'mkdir' cell in the flowchart

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string too long to generate flowchart

I guyess my question should be, how do I stop rendering of the 'mkdir' cell in the flowchart

1/22/17

12/1/16

Ruffus drmaa issue with Python 3

I have been following these instructions, with the eventual aim of getting ruffus to work with LSF.

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Ruffus drmaa issue with Python 3

I have been following these instructions, with the eventual aim of getting ruffus to work with LSF.

12/1/16

Bernard James Pope, Leo Goodstadt 顧維斌3

9/28/16

Running a very large number of tasks with Ruffus over a long period of time

Hi Leo, Thanks for your reply. The dummy tasks is a good idea. After much consideration, I've

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Running a very large number of tasks with Ruffus over a long period of time

Hi Leo, Thanks for your reply. The dummy tasks is a good idea. After much consideration, I've

9/28/16

Chris Rands, Leo Goodstadt3

6/17/16

pipeline_printout_graph not working

Thank you Leo. That would be very helpful. Chris On Thursday, 16 June 2016 14:53:56 UTC+2, Leo

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pipeline_printout_graph not working

Thank you Leo. That would be very helpful. Chris On Thursday, 16 June 2016 14:53:56 UTC+2, Leo

6/17/16

Keith Hughitt, Leo Goodstadt 顧維斌7

4/13/16

Multiple tasks depend on same output from a single task?

Glad to hear it. Leo On 13 April 2016 at 21:04, Keith Hughitt <keith....@gmail.com> wrote:

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Multiple tasks depend on same output from a single task?

Glad to hear it. Leo On 13 April 2016 at 21:04, Keith Hughitt <keith....@gmail.com> wrote:

4/13/16

Olabode Ajayi, Leo Goodstadt 顧維斌2

4/12/16

TRIM_GALORE WITH RUFFUS

Hi Olabode, I am not sure if I understand you. You can use wild cards in your output if you don't

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TRIM_GALORE WITH RUFFUS

Hi Olabode, I am not sure if I understand you. You can use wild cards in your output if you don't

4/12/16

Olabode Ajayi, Leo Goodstadt 顧維斌2

4/12/16

@TRANSFORM: DEALING WITH DIRECTORY

Dear AJ, Does "{path[0]}" already exist? Ruffus does not make directories for you unless so

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@TRANSFORM: DEALING WITH DIRECTORY

Dear AJ, Does "{path[0]}" already exist? Ruffus does not make directories for you unless so

4/12/16

Shangzhong Li, Leo Goodstadt 顧維斌2

4/12/16

email notification for each step in pipeline

Sorry for the late reply. There isn't any provision for either. Would you like to add an issue to

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email notification for each step in pipeline

Sorry for the late reply. There isn't any provision for either. Would you like to add an issue to

4/12/16

Diego Diaz Dominguez, Leo Goodstadt 顧維斌8

3/30/16

problem with Filter and regex

Good to hear that. I am a little curious: Would adding output_dir support for regex confusing? Or was

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problem with Filter and regex

Good to hear that. I am a little curious: Would adding output_dir support for regex confusing? Or was

3/30/16

Olabode Ajayi, … Bernard James Pope3

3/11/16

Task_Cluster_Job Script::: Ruffus and Rubra Infrstructure

Hi Ajayi, Thanks for responding Leo. I'm not sure what is the cause of the problem. However, it

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Task_Cluster_Job Script::: Ruffus and Rubra Infrstructure

Hi Ajayi, Thanks for responding Leo. I'm not sure what is the cause of the problem. However, it

3/11/16

Alejandro Dubrovsky, … Leo Goodstadt 顧維斌11

2/25/16

Decorator that takes function for arbitrary mapping between input and output names

Sorry everyone, I am still working on this. 1. Syntax The actual working of the custom function seems

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Decorator that takes function for arbitrary mapping between input and output names

Sorry everyone, I am still working on this. 1. Syntax The actual working of the custom function seems

2/25/16

2/18/16

Having trouble using collate() with formatter()

Hello, I am struggling to get my head around the collate syntax using formatters. I've made an

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Having trouble using collate() with formatter()

Hello, I am struggling to get my head around the collate syntax using formatters. I've made an

2/18/16

2/14/16

merging FASTQ files

Hi, I have the following file structure with FASTQ files: ~/Downloads/kumaran/reads > tree ├── C5-

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merging FASTQ files

Hi, I have the following file structure with FASTQ files: ~/Downloads/kumaran/reads > tree ├── C5-

2/14/16

2/12/16

Input file does not exist

Hi, I have recieved the following error with running the code below code: ... bowtie2 -x /home/galaxy

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Input file does not exist

Hi, I have recieved the following error with running the code below code: ... bowtie2 -x /home/galaxy

2/12/16

1/11/16

ignore mkdir tasks when drawing flowchart

I have this problem when drawing flowchart using ruffus, it includes all mkdir tasks with names like

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ignore mkdir tasks when drawing flowchart

I have this problem when drawing flowchart using ruffus, it includes all mkdir tasks with names like

1/11/16

Dr Ashwin Kotwaliwale, Leo Goodstadt 顧維斌2

1/8/16

Parallel processing in Ruffus

Dear Ashwin, The obvious way to do this would be something like chromosome_names = map(str, range(1,

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Parallel processing in Ruffus

Dear Ashwin, The obvious way to do this would be something like chromosome_names = map(str, range(1,

1/8/16

Dr Ashwin Kotwaliwale, Leo Goodstadt 顧維斌2

1/6/16

Pass a list of file to ruffus pipeline

Hi Ashwin, I am afraid I don't yet understand your difficulties. Do you have a minimal code

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Pass a list of file to ruffus pipeline

Hi Ashwin, I am afraid I don't yet understand your difficulties. Do you have a minimal code

1/6/16

Karl Nordström, Leo Goodstadt 顧維斌5

9/7/15

content of string in extras disrupts pipeline

It does. The problem must be somewhere here. I did the coding and running through PyDev in Eclipse.

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content of string in extras disrupts pipeline

It does. The problem must be somewhere here. I did the coding and running through PyDev in Eclipse.

9/7/15

Yuichi Shiraishi

8/31/15

about tumor and matched normal comparison

Hi, I'm Yuichi Shiraishi, working at the Univ. Tokyo. We are very interested in incorporating

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about tumor and matched normal comparison

Hi, I'm Yuichi Shiraishi, working at the Univ. Tokyo. We are very interested in incorporating

8/31/15

Jafar Taghiyar, … Peter Ebert4

8/25/15

v2.6.3 ignores the flag files used by @check_if_uptodate and re-runs the task regardless

Hi Leo, just stumbled across this question of yours concerning the use of @parallel and possible

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v2.6.3 ignores the flag files used by @check_if_uptodate and re-runs the task regardless

Hi Leo, just stumbled across this question of yours concerning the use of @parallel and possible

8/25/15

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