thasso pyjip issues - Githubissues

thasso / pyjip

JIP Pipeline System

http://pyjip.readthedocs.org

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issues

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Cannot create mutually exclusive options

#62 necrolyte2 opened 8 years ago
0
TypeError: can't pickle instancemethod objects when including init/validate/setup methods

#61 necrolyte2 opened 8 years ago
0
named pipes/job with 2 outputs

#60 necrolyte2 closed 8 years ago
2
Shebang line on Linux for pipelines does not work

#59 necrolyte2 opened 8 years ago
0
BWA pipeline example code is broken?

#58 d3d1y closed 9 years ago
4
submit does not work on SGE

#57 jdidion opened 10 years ago
2
Python 3 support

#56 piotrbulinski closed 10 years ago
0
Submitting jobs on a remote cluster

#55 jdidion opened 10 years ago
9
Develop

#54 Poshi closed 10 years ago
12
Add MySQL support

#53 emi80 closed 9 years ago
0
Error when try to use development in -q parameter

#52 marcDabad opened 10 years ago
0
Hidden options are not resolved when called explicitly

#51 emi80 closed 9 years ago
0
Specs are not properly processed when being affected by job grouping

#50 Poshi opened 10 years ago
0
New: Check for presence of cluster commands in PATH

#49 Poshi closed 10 years ago
4
Having multiple pipeline instances at same time creates concurrency issues into the database

#48 lfrias81 opened 10 years ago
0
Check called binaries and scream if not found

#47 Poshi closed 10 years ago
1
Add option to select memory unit for SGE

#46 emi80 closed 10 years ago
0
Jip restart: feature request

#45 lfrias81 opened 10 years ago
0
Not good integration with bash arrays in jip tools

#44 lfrias81 opened 10 years ago
0
If a non-existing option is referenced in a script template, an AttributeError is raised

#43 thasso closed 9 years ago
0
Memory for Jobs is set to early to default 0 and can not be changed by the profiles default

#42 thasso opened 10 years ago
0
Release 0.5 breaks with some python recursivity problem

#41 lfrias81 opened 10 years ago
1
Wrong unit for memory when submitting to SGE

#40 emi80 closed 10 years ago
3
Enable rendering of log file location using pipeline and tools options

#39 thasso closed 10 years ago
0
Options embedded in command scripts are not made absolute

#38 thasso closed 10 years ago
0
Make sure that working directories of jobs are created when jobs are executed or submitted

#37 thasso closed 10 years ago
0
Wrong Output --dry

#36 marcDabad opened 10 years ago
0
Allow for dynamic options when a tool is added to a pipeline

#35 thasso closed 10 years ago
1
Configuration is not picked up next to the binary

#34 thasso closed 10 years ago
0
Create a post-validate hook to be able to check the result state of a job manually

#33 thasso opened 10 years ago
0
Expose the extra parameter to job() and all command line tools

#32 thasso opened 10 years ago
0
Log files are not properly resolved on all SGE installations

#31 thasso opened 10 years ago
0
The API example runs the jobs but a jip clear fails on the generated jobs

#30 thasso closed 10 years ago
1
Working directory is not passed on from profile to job

#29 thasso closed 10 years ago
0
Add a thread parameter to the server to control the number of slots

#28 thasso closed 10 years ago
0
make Node.depends_on accept a list of other nodes

#27 thasso closed 10 years ago
0
Option value assignment through options attributes is does not set the value

#26 thasso closed 10 years ago
0
Setup is not called when tools are added to a pipeline

#25 Poshi closed 10 years ago
1
Option descriptions are not handling tabs at the beginning correctly

#24 thasso closed 10 years ago
0
JIP tools script with . in the name are not parsed correctly.

#23 thasso closed 10 years ago
0
Create a pipe command to write quick pipeline directly from the command line

#22 thasso closed 10 years ago
0
The > operator should disable streaming if used between nodes

#21 thasso closed 10 years ago
0
Inconsistency between job().bash() and bash() usage in pipeline

#20 thasso closed 10 years ago
0
Add links to job and pipeline iteration to delete functions in jip.db and jip.jobs

#19 thasso closed 10 years ago
0
Enable parsing of memory assignments in profiles and add support for G M and K suffixes

#18 thasso closed 10 years ago
0
jip bash should accept command script from stdin

#17 thasso closed 10 years ago
0
"jip logs" called without argument returns an error instead of "usage"

#16 fransua closed 10 years ago
1
Add description (optional) field in profiles

#15 fransua closed 10 years ago
1
Add option to cut full extensions with the ext filter

#14 thasso closed 10 years ago
0
Log file names are not rendered and populated with options

#13 thasso closed 10 years ago
0