Ensembl / ensembl-compara / 81
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release/98: 63%

LAST BUILD BRANCH: release/102
DEFAULT BRANCH: release/98
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Jobs 1
Files 165
Run time 1min
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Merge branch 'feature/update_pipeline'

* feature/update_pipeline: (44 commits)
  Mafft_update dumps the alignment in the right format
  Safer call to GeneAlignAdaptor::store()
  The tags are stored in the correct clusterset
  New "aln_clusterset_id" parameter to define the clusterset_id of the alignment
  API change: new method to handle alternative trees
  It is safe to call preload() multiple times
  Reverted the indentation to its initial state
  Refactored the target_tree handling in GenericRunnable
  The tree has already been stored, no need to minimize it at this stage
  These parameters are actually not used
  Revert "Correcting some identation issues."
  We make sure that the updated alignment does not contain extra rows that should have been removed
  A better name is "force_new_alignment"
  Revert "New flag UPDATE_ALIGNMENT added."
  Species trees containing only mammals+baboon
  Added papio_anubis
  Change in the command line 'cmd'. We had a 'sed' call in order to filter the outputs. But that is not necessary since the raxml command we are using does not include any characters in the resulting trees.
  Change in fetch_input, making the tree adaptor fetch the correct tree (copy_tree), and dump the correct alignment (copy_tree) to the working dir. Fetch the tags from gene_tree_root_tag for: current_gene_tree && current_gene_tree, and use them to creat the file conatining the "new" sequences to be added. Remove unnecessary dependency. Added a few parameters to the param_defaults
  Added param_defaults function, so that we can undef 'aln_update' Added control for 'aln_update', so that: 1 - we use the get_GeneAlignAdaptor correctly 2 - we run load_cigars_from_file with the correct parameters.
  Added a param for storing the copy_gene_tree. We should obtail all the alignment related data from the copy_gene_tree, so the change off all the objects refering current_gene_tree to copy_gene_tree.
  ...

Conflicts:
	modules/Bio/EnsEMBL/Compara/PipeConfig/Example/TFProteinTrees_conf.pm

10135 of 24732 relevant lines covered (40.98%)

875.28 hits per line

Jobs
ID Job ID Ran Files Coverage
2 81.2 (COVERALLS=true) 0
40.98
 Travis Job 81.2
Source Files on build 81
Detailed source file information is not available for this build.