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thasso
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pyjip
JIP Pipeline System
http://pyjip.readthedocs.org
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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
9 years ago
2
Python 3 support
#56
piotrbulinski
closed
9 years ago
0
Submitting jobs on a remote cluster
#55
jdidion
opened
9 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
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