Commit 91d9530d authored by Leo Gordon's avatar Leo Gordon
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latest changes

parent db651912
......@@ -17,6 +17,52 @@ Summary:
the graphs but could be adapted more generally.
11 May, 2010 : Leo Gordon
* We finally have a universal framework for commandline-configurable pipelines' setup/initialization.
Each pipeline is defined by a Bio::EnsEMBL::Hive::PipeConfig module
that derives from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf .
Compara pipelines derive from Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf .
These configuration modules are driven by ensembl-hive/scripts/init_pipeline.pl script.
Having set up what is an 'option' in your config file, you can then supply values for it
from the command line. Option interdependency rules are also supported to a certain extent,
so you can supply *some* options, and rely on the rules to compute the rest.
* Several example PipeConfig files have been written to show how to build pipelines both 'standard blocks'
(SystemCmd, SqlCmd, JobFactory, Dummy, etc) and from RunnableDBs written specifically for the task
(components of LongMult pipeline).
* Both eHive RunnableDB::* and PipeConfig::* modules have been POD-documented.
* A new 'input_id_template' feature has been added to the dataflow mechanism to allow for more flexibility
when integrating external scripts or unsupported software into eHive pipelines.
You can now dataflow from pretty much anything, even if the Runnable did not support dataflow natively.
The corresponding schema patch is in ensembl-hive/sql
* pipeline-wide parameters (kept in 'meta' table) no longer have to be scalar.
Feel free to use arrays or hashes if you need them. init_pipeline.pl also supports multilevel options.
* SqlCmd now has a concept of 'sessions': you can supply several queries in a list that will be executed
one after another. If a query creates a temporary table, all the following ones down the list
will be able to use it.
* SqlCmd can run queries against any database - not necessarily the eHive one. You have to supply a hashref
of connection parameters via $self->param('db_conn') to make it work. It still runs against the eHive
database by default.
* JobFactory now supports 4 sources: inputlist, inputfile, inputquery and inputcmd.
*All* of them now support deep param_substitution. Enjoy.
* NB! JobFactory's substituted parameter syntax changed:
it no longer understands '$RangeStart', '$RangeEnd' and '$RangeCount'.
But it understands '#_range_start#', '#_range_end#' and '#_range_count#' - should be pretty easy to fix.
* several smaller bug fixes and optimizations of the code have also been done.
A couple of utility methods have moved places, but it looks like they were mostly used internally.
Shout if you have lost anything and we'll try to find it together.
26 March, 2010 : Leo Gordon
* branch_code column in analysis_job table is unnecessary and was removed
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