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1–30 of 65
BDS Discussions and Showcasing of Pipelines. Please use
https://github.com/
pcingola/BigDataScript
to submit bugs and see source code.
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Aimin Yan
,
pablo.e....@gmail.com
2
8/15/20
run BDS on AWS
A few comments here: 1) You are stating that each task requires 32 cpus, so to run 3 in parallel you
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run BDS on AWS
A few comments here: 1) You are stating that each task requires 32 cpus, so to run 3 in parallel you
8/15/20
JAVAN OKENDO
,
Kirill Tsyganov
3
3/25/20
New user here
Dear Kirill, Thanks for your generous response. It's helpful and I hope it will get me started On
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New user here
Dear Kirill, Thanks for your generous response. It's helpful and I hope it will get me started On
3/25/20
haris zaf
8/5/19
bds.pid file - error
Hi all! I am running a .bds script in a Linux environment and everything is going fine. Then, I am
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bds.pid file - error
Hi all! I am running a .bds script in a Linux environment and everything is going fine. Then, I am
8/5/19
haris zaf
2/13/19
checkpoint path
Hi, I d like to know whether is it possible to set the path where the checkpoint is being created.
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checkpoint path
Hi, I d like to know whether is it possible to set the path where the checkpoint is being created.
2/13/19
haris zaf
2/8/19
BDS in Singularity Image
Hi all, I am trying to run a .bds script through Singularity. In my Singularity image there are some
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BDS in Singularity Image
Hi all, I am trying to run a .bds script through Singularity. In my Singularity image there are some
2/8/19
haris zaf
,
Kirill Tsyganov
3
11/21/18
running tools through a BDS script inside Docker container
Hi Kirill and thank you for your reply! It was a bad bug. A simple script as you said, it was ok and
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running tools through a BDS script inside Docker container
Hi Kirill and thank you for your reply! It was a bad bug. A simple script as you said, it was ok and
11/21/18
Aimin Yan
, …
Kirill Tsyganov
3
11/5/18
Difference between BDS and Cromwell + WDL
Hi all, Kyle answers your question exactly, from what I can tell. I just want to through a bit extra
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Difference between BDS and Cromwell + WDL
Hi all, Kyle answers your question exactly, from what I can tell. I just want to through a bit extra
11/5/18
aimin....@gmail.com
, …
Pablo Cingolani
11
10/6/18
use multiple input files to generate one output file
Many people use BDS on the head node. The error looks simply like a memory allocation issue (Iethe
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use multiple input files to generate one output file
Many people use BDS on the head node. The error looks simply like a memory allocation issue (Iethe
10/6/18
Chi Pak
,
Kirill Tsyganov
2
6/29/18
SLURM
Hi, You specify them in the bds.config. We use SLURM and this is our bds.config mem = 16G retry = 1
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SLURM
Hi, You specify them in the bds.config. We use SLURM and this is our bds.config mem = 16G retry = 1
6/29/18
aimin....@gmail.com
,
Pablo Cingolani
2
6/8/18
Q&A
About Task Graph
This figure hasn't been working properly for some time. Hopefully I'll get the chance to fix
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Q&A
About Task Graph
This figure hasn't been working properly for some time. Hopefully I'll get the chance to fix
6/8/18
Chi Pak
,
Pablo Cingolani
3
5/30/18
arithmetic bug?
Fixed in release "2.0 rc 7" (from master). Thank you for reporting. On Mon, May 28, 2018 at
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arithmetic bug?
Fixed in release "2.0 rc 7" (from master). Thank you for reporting. On Mon, May 28, 2018 at
5/30/18
aimin....@gmail.com
, …
Pablo Cingolani
17
5/9/18
bds install
I'm glad to hear that it worked out. On Wed, May 9, 2018, 1:48 PM Aimin Yan <aimin.at.work@
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bds install
I'm glad to hear that it worked out. On Wed, May 9, 2018, 1:48 PM Aimin Yan <aimin.at.work@
5/9/18
aimin....@gmail.com
,
Kirill Tsyganov
2
4/24/18
test bds on cluster
broken syntax, looks like you missing an if statement and braket? On Wed, 25 Apr 2018, 10:24 <
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test bds on cluster
broken syntax, looks like you missing an if statement and braket? On Wed, 25 Apr 2018, 10:24 <
4/24/18
aimin....@gmail.com
, …
Kirill Tsyganov
3
4/23/18
Q&A
find the matched files with certain pattern recursively
Hi Aimin, This is my implementation of the recursive function https://github.com/
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Q&A
find the matched files with certain pattern recursively
Hi Aimin, This is my implementation of the recursive function https://github.com/
4/23/18
Chi Pak
,
Pablo Cingolani
2
4/3/18
dependency operator behavior - left hand argument is size-0 array
In the dependency operator, the outputs (left-hand side) depends on the inputs (right-hand side). If
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dependency operator behavior - left hand argument is size-0 array
In the dependency operator, the outputs (left-hand side) depends on the inputs (right-hand side). If
4/3/18
Chi Pak
,
Pablo Cingolani
3
2/12/18
store as variable - number-of-lines of file
Thanks, that did the trick On Monday, February 12, 2018 at 11:28:37 AM UTC-6, Pablo Cingolani wrote:
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store as variable - number-of-lines of file
Thanks, that did the trick On Monday, February 12, 2018 at 11:28:37 AM UTC-6, Pablo Cingolani wrote:
2/12/18
Chi Pak
,
Pablo Cingolani
3
1/3/18
Q&A
switch - type comparison
Thanks Pablo. Happy New Year to you too! On Wednesday, January 3, 2018 at 9:42:15 AM UTC-6, Pablo
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Q&A
switch - type comparison
Thanks Pablo. Happy New Year to you too! On Wednesday, January 3, 2018 at 9:42:15 AM UTC-6, Pablo
1/3/18
Chi Pak
,
Pablo Cingolani
2
11/2/17
filter list (of filenames) based on other list (of look_for vars)
You can use dirname.dir( string_glob ) Here is your example adjusted: #!/usr/bin/env bds vars := [
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filter list (of filenames) based on other list (of look_for vars)
You can use dirname.dir( string_glob ) Here is your example adjusted: #!/usr/bin/env bds vars := [
11/2/17
Chi Pak
,
Kirill Tsyganov
3
10/9/17
experimental design file
Thanks a lot Kirill! It makes sense why my original code wasn't working. I'll implement your
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experimental design file
Thanks a lot Kirill! It makes sense why my original code wasn't working. I'll implement your
10/9/17
Chi Pak
,
Kyle Hernandez
3
9/13/17
string.dir(regex) issue
Haha, of course. I've become too used to using grep(). Thanks. On Wednesday, September 13, 2017
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string.dir(regex) issue
Haha, of course. I've become too used to using grep(). Thanks. On Wednesday, September 13, 2017
9/13/17
Chi Pak
, …
Pablo Cingolani
7
9/1/17
dependency question - one output file depends on multiple input files
Ahh, yes. Zero-byte files are considered errors because we want to catch when commands fail to create
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dependency question - one output file depends on multiple input files
Ahh, yes. Zero-byte files are considered errors because we want to catch when commands fail to create
9/1/17
nieh...@gmail.com
,
Kyle Hernandez
5
7/22/17
Q&A
Run job on a cluster
Yes, the job id was "19284721.node43". I set pidRegex to "(\\d+\\.node\\d+)" When
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Q&A
Run job on a cluster
Yes, the job id was "19284721.node43". I set pidRegex to "(\\d+\\.node\\d+)" When
7/22/17
Pablo Cingolani
7/8/17
Re: iterate through matched-elements in two arrays in for loop
How about something like this: path := '.' var := path.dir() # Swap extensions for all files
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Re: iterate through matched-elements in two arrays in for loop
How about something like this: path := '.' var := path.dir() # Swap extensions for all files
7/8/17
Florian Kiefer
,
Pablo Cingolani
3
4/27/17
SGE/UGE cluster implementation
Hi Pablo, thanks for the effort. In the meantime, I found a solution by using a "generic"
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SGE/UGE cluster implementation
Hi Pablo, thanks for the effort. In the meantime, I found a solution by using a "generic"
4/27/17
Chi Pak
,
Kyle Hernandez
3
3/8/17
real to integer to string
Hey Kyle: Thanks for the response. Pablo got back to me with this response: str := "100" #
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real to integer to string
Hey Kyle: Thanks for the response. Pablo got back to me with this response: str := "100" #
3/8/17
Tim Boyarski
, …
Pablo Cingolani
17
2/15/17
Q&A
Questions about BDS features.
Hi Pablo, I see what you have done here. It may join things together too rigidly. Interchangeability
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Q&A
Questions about BDS features.
Hi Pablo, I see what you have done here. It may join things together too rigidly. Interchangeability
2/15/17
Chi Pak
,
Kyle Hernandez
5
2/8/17
IF...IF ELSE...ELSE
Ok, that's great. I didn't see any instance where ELSE IF was used in the Documentation. I
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IF...IF ELSE...ELSE
Ok, that's great. I didn't see any instance where ELSE IF was used in the Documentation. I
2/8/17
Chi Pak
2/7/17
define BOOLEAN, set as conditional
Hi: I'd like to define a BOOLEAN, and then use it in a conditional IF...THEN So here's sample
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define BOOLEAN, set as conditional
Hi: I'd like to define a BOOLEAN, and then use it in a conditional IF...THEN So here's sample
2/7/17
Chi Pak
2/7/17
OR or AND conditionals?
Hi: I was wondering if BDS supports OR (OR, |, ||) or AND (AND, &, &&) conditionals in IF
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OR or AND conditionals?
Hi: I was wondering if BDS supports OR (OR, |, ||) or AND (AND, &, &&) conditionals in IF
2/7/17
Chi Pak
, …
Pablo Cingolani
4
2/3/17
pipe not being read?
Hi Pablo: I solved my general issue (reading in parameters from external file) with config(). Super
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pipe not being read?
Hi Pablo: I solved my general issue (reading in parameters from external file) with config(). Super
2/3/17