<commit_before>
This document describes how to run ensembl-compara ProteinTrees pipeline.

1. Dependencies

   1.1 Necessary software components:

	* MySQL 5.1          (or higher)
	* Perl 5.10          (or higher)
	* Perl DBI API 1.6   (or higher)

EnsEMBL and BioPerl software:
	* bioperl-live (version 1.6.9)               - Base of the BioPerl distribution. Mainly needed to provide I/O for alignments
	* bioperl-run (version 1.6.9)                - Needed for the CodeML runnable/parser
	* ensembl ("release/76" branch)              - Core API on which the rest of ensembl APIs are based
	* ensembl-compara ("release/76" branch)      - Compara API (data objects, db adaptors, pipeline runnables, pipeline configuration)
	* ensembl-hive ("version/2.0" branch)        - The system to run pipelines. Note that the pipeline is also compatible with the version/2.1 branch

Refer to the following pages for tips about installation and setting up the environment:
	http://www.ensembl.org/info/docs/api/api_installation.html
	http://www.ensembl.org/info/docs/eHive/installation.html

!! Please ensure that your PERL5LIB includes all of these modules and $ENSEMBL_CVS_ROOT_DIR points to the location of the checkouts !!

Perl libraries:

	 (mandatory)
	* Statistics::Descriptive    - Used during the dN/dS computation
	* Parse::RecDescent          - To export trees in newick

	 (optional)
	* JSON                       - Used to configure the non-Ensembl species on which the pipeline has to run
	* FamLibBuilder              - Only needed for the HMM-based clustering. Part of the Panther distribution
	* XML::Writer                - Used to output trees in OrthoXML and PhyloXML


Any compiled binaries mentioned in ensembl-compara/modules/Bio/EnsEMBL/Compara/PipeConfig/Example/EnsemblProteinTrees_conf.pm
Here is the list of the versions that we used for the e76 production:

	* NCBI-blast 2.2.28+   - ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
	* mcoffee 9.03.r1318   - http://www.tcoffee.org/Projects/mcoffee/
	* MAFFT 7.113          - http://mafft.cbrc.jp/alignment/software/
	* hcluster_sg          - http://treesoft.svn.sourceforge.net/viewvc/treesoft/branches/lh3/hcluster/
	* treebest             - https://github.com/muffato/treebest<commit_msg>pipeline not compatible with eHive 2.1<commit_after>
This document describes how to run ensembl-compara ProteinTrees pipeline.

1. Dependencies

   1.1 Necessary software components:

	* MySQL 5.1          (or higher)
	* Perl 5.10          (or higher)
	* Perl DBI API 1.6   (or higher)

EnsEMBL and BioPerl software:
	* bioperl-live (version 1.6.9)               - Base of the BioPerl distribution. Mainly needed to provide I/O for alignments
	* bioperl-run (version 1.6.9)                - Needed for the CodeML runnable/parser
	* ensembl ("release/76" branch)              - Core API on which the rest of ensembl APIs are based
	* ensembl-compara ("release/76" branch)      - Compara API (data objects, db adaptors, pipeline runnables, pipeline configuration)
	* ensembl-hive ("version/2.0" branch)        - The system to run pipelines. Note that this version of the pipeline is *not* compatible with the eHive version/2.1 branch

Refer to the following pages for tips about installation and setting up the environment:
	http://www.ensembl.org/info/docs/api/api_installation.html
	http://www.ensembl.org/info/docs/eHive/installation.html

!! Please ensure that your PERL5LIB includes all of these modules and $ENSEMBL_CVS_ROOT_DIR points to the location of the checkouts !!

Perl libraries:

	 (mandatory)
	* Statistics::Descriptive    - Used during the dN/dS computation
	* Parse::RecDescent          - To export trees in newick

	 (optional)
	* JSON                       - Used to configure the non-Ensembl species on which the pipeline has to run
	* FamLibBuilder              - Only needed for the HMM-based clustering. Part of the Panther distribution
	* XML::Writer                - Used to output trees in OrthoXML and PhyloXML


Any compiled binaries mentioned in ensembl-compara/modules/Bio/EnsEMBL/Compara/PipeConfig/Example/EnsemblProteinTrees_conf.pm
Here is the list of the versions that we used for the e76 production:

	* NCBI-blast 2.2.28+   - ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
	* mcoffee 9.03.r1318   - http://www.tcoffee.org/Projects/mcoffee/
	* MAFFT 7.113          - http://mafft.cbrc.jp/alignment/software/
	* hcluster_sg          - http://treesoft.svn.sourceforge.net/viewvc/treesoft/branches/lh3/hcluster/
	* treebest             - https://github.com/muffato/treebest
{'fraction_non_alphanumeric': 0.08562091503267974, 'fraction_numerical': 0.01917211328976035, 'mean_word_length': 2.9005947323704335, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 6, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7235946', 'n_tokens_mistral': 1529, 'n_tokens_neox': 1398, 'n_words': 452}