Biolite

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* Improved poor I/O performance of BioLite tools. (42)
* New 'bl-examl-bootstraps' script for automating ExaML runs. (agalma-issue-155)
* Added support for 454 data to SRA export. (39)
* Merged Agalma and BioLite sqlite files, and moved agalma.database functions
into biolite.database. (agalma-issue-162)
* Removed default database path from biolite.cfg, to support AGALMA_DB.
(agalma-issue-164)
* Added probabilistic subsampling in filter-illumina. (44)
* Removed 'outdir' and relocated permanent storage to database.
(agalma-issue-163)
* Scalability improvements for large analyses. (agalma-issue-174)
* Updated Trinity wrapper to support 2.1.1. (agalma-issue-188)
* Added infrastructure for unit tests with pytest. (46)
* Fixed bug in paralogy prune: not pruning all subtrees. (48)
* New workflow for phylogenetically guided assembly. (agalma-issue-203)
* Updated dendropy to latest version 4. (agalma-issue-207)
* Changes to utils.md5seed() for genetrees update. (agalma-issue-214)
* Added pandas support for reports. (agalma-issue-220)
* Conda recipes for BioLite and its dependencies. (agalma-issue-227)

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* New catalog schema with 'treatment' and 'individual' fields, to support
phylogenetic analyses of gene expression. (agalma-issue-103)
* Additional features in tabular reports and additional wrappers to support
a chloroplast assembly project. (35)
* Modified transcriptome workflows and added support for the latest version of the
Trinity RNA-seq assembler. (agalma-issue-127)
* Replaced SRA samples with BioSamples in 'bl-sra export'. (34)
* The 'diagnostics' module can now be used without a connection to a BioLite
dabatase and without initializing a run ID. All diagnostics messages are printed
to 'stderr' instead of to the diagnostics database. (30)
* Updated paths in the 'transcriptome.quantify' workflow to make use of data vs.
scratch storage. (agalma-issue-141)
* Added support for gzipped files to 'utils.head_to_file'. (agalma-issue-129)
* Fixed bug with workflows that used an incorrect default value for the 'workdir'
optional argument. (38)
* Added a 'title' field to the 'rRNAhit' struct in the rrna workflows.
(agalma-issue-134)

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* Switched the build system for the Python module from GNU autotools to Python
distutils. The Python module can now be installed with pip, the Python
package manager. The C++ tools are now packaged separately (and located in the
'tools' subdir of the repo) and still use GNU autotools. The Python module
works independently of the C++ tools, and the tools are only necessary if a
pipeline calls one of them through a wrapper, i.e. the tools are now an
optional dependency like the other third-party tools that BioLite provides
wrappers for. (25)
* BioLite scripts and tools are now prefixed with `bl-` to avoid polluting the
PATH, i.e. `diagnostics` is now `bl-diagnostics`.
* Removed 'build_3rd_party.sh' script. All third-party tools can now be installed
with Bioinformatics Brew (https://bib.bitbucket.org), including the
'biolite-tools' package.
* Cleaned up supermatrix workflow. (agalma-issue-54)
* Added wrappers for running RAxML with MPI. (agalma-issue-115)
* Improved Illumina header detection in the catalog. (agalma-issue-93)
* New standardized header format in the transcriptome workflows. (agalma-issue-116)

=======

* Updated URL for transdecoder (file was moved).

=====

* Hotfixes for incorrect y-axis scaling in report.histogram_overlay() and for
SVG output in report.imageplot().
* Updated the versions of Trinity (2013-08-14) and RAxML (v7.7.6) in
build_3rd_party.sh, added MAFFT, and fixed a relative path issue with OMA.
* Bug fixes in 'report' and 'workflows', new wrappers, new features in
'diagnostics' and 'pipeline', and other improvements to support Agalma 0.3.5.

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* Improved support for multi-node (distributed) processing using GNU parallel.
(12)
* New schema for `runs` table improves performance of `diagnostics list`. (9)
* Merged in a more flexible wrapper base class (as `wrappers2`) from an earlier
branch of BioLite developed for the `chlororef` project. New wrappers will
most likely be implemented in `wrappers2` and all existing wrappers will
gradually be migrated to the new base class. (20)
* Additional wrappers and minor features to support improvements in Agalma
0.3.4.