Package: pyjip
JIP Pipeline systemThe JIP pipeline system is a python library and a set of command
line utilities that allows you to create batch-process based computational
pipeline that can be submitted and managed on a compute cluster or on
your local machine.InstallationTheJIP documentationcontains
more detailed instructions on installation and, more importantly, configuration
of the system and your compute infrastructure. Here is the very quick guide:$> pip install pyjip

or

$> python setup.py installIf you want to install frompypior the git repository. Afterwards, you have
to create configuration file$HOME/.jip/jip.jsonand add the following
content:{
    "cluster": "<class_name>"
}Replace<class_name>with the name of the class that implements support
for your compute cluster. JIP ships with the following implementations:jip.cluster.SGEforSun Grid Enginejip.cluster.SlurmforSlurmjip.cluster.PBSforPBSandTorquejip.cluster.LSFforPlatform LSFandOpen Lavajip.grids.JIPfor JIPs’ internal scheduler. If you use this, make
sure to start the JIP server on the same machine using thejip servercommand. Please note also that you have to installpyzmqif you want
to run the JIP server.DocumentationDocumentationon installation and
usage can be found athttp://pyjip.readthedocs.org/en/latest/.Source CodeThe JIP source code can be found onGitHub.Bugs and feature requestsPlease feel free to use theissue trackerto file bug reports and feature
requests.Changelog0.6:Add MySQL support [Issue #53]Hidden options are not resolved when called explicitly [Issue #51]Add option to select memory unit for SGE [Issue #46]If a non-existing option is referenced in a script template, an AttributeError is raised [Issue #43]Wrong unit for memory when submitting to SGE [Issue #40]0.5:Enable rendering of log file location using pipeline and tools options [Issue #39]Options embedded in command scripts are not made absolute [Issue #38]Make sure that working directories of jobs are created when jobs are executed or submitted [Issue #37]Allow for dynamic options when a tool is added to a pipeline [Issue #35]Configuration is not picked up next to the binary [Issue #34]The API example runs the jobs but a jip clear fails on the generated jobs [Issue #30]Working directory is not passed on from profile to job [Issue #29]Add a thread parameter to the server to control the number of slots [Issue #28]Option value assignment through options attributes is does not set the value [Issue #26]Option descriptions are not handling tabs at the beginning correctly [Issue #24]JIP tools script with . in the name are not parsed correctly.  [Issue #23]Restarting a single job pipeline and changeing the threads is not reflected in the job [Issue #6]Make tool specs available to pipelines [Issue #4]0.4:Create a pipe command to write quick pipeline directly from the command line [Issue 22]Inconsistency between job().bash() and bash() usage in pipeline [Issue 20]Add links to job and pipeline iteration to delete functions in jip.db and jip.jobs [Issue 19]Enable parsing of memory assignments in profiles and add support for G M and K suffixes [Issue 18]“jip logs” called without argument returns an error instead of “usage” [Issue 16]Tool cleanup fails if the output points to a directory [Issue 10]Option parsing fails when multiple list options are specified and one is optional and not set [Issue 8]jip restart jobs fails as the job detects itself and refuses to submit again [Issue 7]jip jobs with selected output duplicates columns [Issue 5]0.3 :Added auto-naming support for anonymous jobs that are assigned to variables.
The variable name is used as default job nameLots of changes to the internals0.2 :Added explicit UTF-8 encoding for the dependency tree0.1 : Initial releaseLicencesJIP is licensed under the BSD license.