pallassgj bpipe issues - Githubissues

pallassgj / bpipe

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Parallel segments utilizing the same stage mix up outputs if run with low thread constraint

#59 GoogleCodeExporter closed 9 years ago
3
run bpipe in parallel

#58 GoogleCodeExporter opened 9 years ago
3
Same stage used with multiple different parameters in parallel causes errors

#57 GoogleCodeExporter closed 9 years ago
2
Input variable with extension sometimes references wrong files in parallel pipeline

#56 GoogleCodeExporter closed 9 years ago
2
Problem executing commands with backslash

#55 GoogleCodeExporter opened 9 years ago
2
Transform should not overwrite input files if output file would be produced with same name as input

#54 GoogleCodeExporter opened 9 years ago
0
Consecutive parallel segments cause unexpected multiple execution of stages

#53 GoogleCodeExporter closed 9 years ago
1
Bpipe run fails

#52 GoogleCodeExporter opened 9 years ago
5
Documentation update

#51 GoogleCodeExporter closed 9 years ago
2
Execute multiline commands

#50 GoogleCodeExporter opened 9 years ago
2
Pause Command

#49 GoogleCodeExporter opened 9 years ago
0
Error Displayed if Run Pipeline with HTML Report but no Stages Execute

#48 GoogleCodeExporter closed 9 years ago
0
bpipe log executed as different user to the one who started the pipeline incorrectly reports that it is finished

#47 GoogleCodeExporter opened 9 years ago
0
Bpipe should support OAuth for Accessing Google Services

#46 GoogleCodeExporter opened 9 years ago
1
Error Displayed when referring to an Unknown Pipeline Stage is Ugly

#45 GoogleCodeExporter closed 9 years ago
1
Simple stage execution make Bpipe crash when launched twice in row

#44 GoogleCodeExporter closed 9 years ago
2
Support for Child Directories for Outputs of Pipeline Stages

#43 GoogleCodeExporter opened 9 years ago
4
Merged job logging of parallel commands.

#42 GoogleCodeExporter opened 9 years ago
2
Job id missing from commandlog.txt

#41 GoogleCodeExporter closed 9 years ago
3
Passing Parameters with 'Using' Broken

#40 GoogleCodeExporter closed 9 years ago
3
Splitting to Parallel Paths by Chromosome not Working at End of Pipeline

#39 GoogleCodeExporter closed 9 years ago
1
Ability to Pass Command Line Options to Script

#38 GoogleCodeExporter closed 9 years ago
1
Input Splitting not Working Correctly on Some Patterns

#37 GoogleCodeExporter closed 9 years ago
1
Support "include" statement

#36 GoogleCodeExporter closed 9 years ago
5
About the frequency of polling job status

#35 GoogleCodeExporter opened 9 years ago
7
Not Work for Symbolic link to bpipe

#34 GoogleCodeExporter closed 9 years ago
4
Trailing Variable Assignment inside Produce Causes Incorrect Inputs Passed to next Stage

#33 GoogleCodeExporter closed 9 years ago
1
Forward not working inside Transform / Filter / Produce

#32 GoogleCodeExporter closed 9 years ago
4
Running bpipe stop reports stopping many more commands than it should

#31 GoogleCodeExporter closed 9 years ago
1
Possible deadlock

#30 GoogleCodeExporter closed 9 years ago
1
ConcurrentModificationException when Running Parallel Pipeline

#29 GoogleCodeExporter closed 9 years ago
1
Ability to Parameterize Pipeline Stages

#28 GoogleCodeExporter closed 9 years ago
1
Ability to Detect and Record the Versions of Tools that Run

#27 GoogleCodeExporter closed 9 years ago
1
Bpipe configuration defaults

#26 GoogleCodeExporter closed 9 years ago
1
Support for Report of Run in HTML Form

#25 GoogleCodeExporter closed 9 years ago
1
Error in Parallelizing same task with different inputs

#24 GoogleCodeExporter opened 9 years ago
3
Transform and Filter should accept multiple arguments

#23 GoogleCodeExporter closed 9 years ago
1
Returning an Object from a Pipeline Stage Should not be Treated as an Output

#22 GoogleCodeExporter closed 9 years ago
1
More generalized form of Parallelization than Splitting by Chromosome

#21 GoogleCodeExporter opened 9 years ago
3
Errors printed out when Bpipe run in Directory for First Time

#20 GoogleCodeExporter closed 9 years ago
1
Support for Email and other Notifications about Pipeline Progress

#19 GoogleCodeExporter opened 9 years ago
1
Support for an easy way to parallelize based on region

#18 GoogleCodeExporter opened 9 years ago
1
Composable Pipelines - Ability to Define Reusable Pipeline Segments

#17 GoogleCodeExporter closed 9 years ago
2
Ability to resolve multiple files using input variable with extensions

#16 GoogleCodeExporter closed 9 years ago
2
Output from commands like 'bpipe test' or printing help should not become the most recent log

#15 GoogleCodeExporter closed 9 years ago
1
Support for Detecting when Commands have Changed in Rerunning Pipeline

#14 GoogleCodeExporter closed 9 years ago
2
Bpipe should offer some way to control how many threads it will create

#13 GoogleCodeExporter closed 9 years ago
1
Deadlock and Corrupted Command Log when running huge number of Parallel Stages (>100)

#12 GoogleCodeExporter closed 9 years ago
1
'bpipe log' shows output from runs even when Bpipe didn't successfully start

#11 GoogleCodeExporter closed 9 years ago
3
Support for "module load" in torque scripts

#10 GoogleCodeExporter opened 9 years ago
4

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