release v0.4.0

doc/Release.rst

@@ -2,90 +2,14 @@
 Release notes
 =============
 
-The CGAT pipelines have not been published yet. Please use the latest version from the repository.
+Notes on each release are below.
 
-0.3.2
------
-
-* removed GCProfile calls from pipelines; https://github.com/CGATOxford/CGATPipelines/pull/368
-* updated installation; https://github.com/CGATOxford/CGATPipelines/pull/370, https://github.com/CGATOxford/CGATPipelines/pull/371, https://github.com/CGATOxford/CGATPipelines/pull/372, https://github.com/CGATOxford/CGATPipelines/pull/375, https://github.com/CGATOxford/CGATPipelines/pull/377
-* pipeline_readqc.py: call cgat script with cgat command; https://github.com/CGATOxford/CGATPipelines/pull/374
-* PipelineMapping.py: fix so star will work with muti QC; https://github.com/CGATOxford/CGATPipelines/pull/376
-* code changes for improved portability of pipelines; https://github.com/CGATOxford/CGATPipelines/pull/380
-* create Python 2 environments for legacy dependencies; https://github.com/CGATOxford/CGATPipelines/pull/381
-* re-factored pipeline_annotations and pipeline_mappinginto pipeline_genesets and pipeline_bamstats respectively; https://github.com/CGATOxford/CGATPipelines/pull/373
-
-0.3.1
------
-
-* fixes for building the docs
-* pipeline_peakcalling: changed default blacklist path; https://github.com/CGATOxford/CGATPipelines/pull/345
-* pipeline_peakcalling: bedGraphToBigWig in new environment requires sorted input; https://github.com/CGATOxford/CGATPipelines/pull/346
-* pipeline_peakcalling: debugging for python 3 in peakcalling notebook reports and changing default format to python 3; https://github.com/CGATOxford/CGATPipelines/pull/347
-* added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh
-* pipeline_peakcalling: added an additional plotting function to generate summary plots after IDR; https://github.com/CGATOxford/CGATPipelines/pull/348
-* pipeline_peakcalling: redirected optimal peaks and conservative peaks to filtered IDR output; https://github.com/CGATOxford/CGATPipelines/pull/349
-* pipeline_rnaseqqc: added functions to check the strandedness of the library, which is required as an input for various mappers; https://github.com/CGATOxford/CGATPipelines/pull/351
-* remove unused imports with autoflakes; https://github.com/CGATOxford/CGATPipelines/pull/354
-* bugfix the way bowtie2 index folder is configured in pipeline_mapping; https://github.com/CGATOxford/CGATPipelines/pull/356 and https://github.com/CGATOxford/CGATPipelines/pull/361
-* bowtie should not use the quite option so multiqc reports properly; https://github.com/CGATOxford/CGATPipelines/pull/357
-* pipeline_peakcalling: minor bugfix; https://github.com/CGATOxford/CGATPipelines/pull/358
-* pipeline_peakcalling: update to work with sicer in a Python 2 environment ; https://github.com/CGATOxford/CGATPipelines/pull/359
-* added **cgatflow** command; https://github.com/CGATOxford/CGATPipelines/pull/360
-* updated documentation and moved unused code to obsolete folder; https://github.com/CGATOxford/CGATPipelines/pull/362
-* updated installation; https://github.com/CGATOxford/CGATPipelines/pull/363 ; https://github.com/CGATOxford/CGATPipelines/pull/367
-* pipeline_peakcalling: update the way IDR is called so it is included as a conda dependency ; https://github.com/CGATOxford/CGATPipelines/pull/364
-
-0.3.0
------
-
-* First release working in Python 3 only.
-
-0.1.1
------
-
-* Last release compatible with Python 2.7
-
-0.1
----
-
-* Re-organize Pipeline.py as a package.
-* Move legacy pipelines OPTIC and GPIPE into separate repository.
-* Distribute contents of PipelineUtilities to CGAT code collection.
-* Revise documentation for modules and scripts.
-
-Contributions
+Release 0.4.0
 =============
 
-We included publicly and freely available code into the tool
-collection for convenience. 
-
-* IGV.py was written by Brent Pedersen.
-* SVGdraw.py was written by ...
-* The NCL module draws from code written by ...
-* list_overlap.py
-* Iterators.py
-
-Contributors
-============
-
-Andreas Heger
-Antonio Berlanga-Taylor
-Martin Dienstbier
-Nicholas Ilott
-Jethro Johnson
-Katherine Fawcett
-Stephen Sansom
-David Sims
-Ian Sudbery
-Hu Xiaoming
-Thomas Smith
-Michael Morgan
-Katherine Brown
-Charlotte George
-Adam Cribbs
-Hania Pavlou
-Reshma Nibhani
-Jakub Scaber
-Sebastian Luna-Valero
+* update installation and conda environments ; https://github.com/cgat-developers/cgat-flow/pull/6
+* migrate pipelines from ini to yml configuration files ; https://github.com/cgat-developers/cgat-flow/pull/11
+* update conda from 4.3 to 4.5 (solving "CXXABI_1.3.9 not found" error ; https://github.com/ContinuumIO/anaconda-issues/issues/5191) ; https://github.com/cgat-developers/cgat-flow/compare/122752d1d380...e7f4a3a166bc
+* add exportdir when missing in pipeline.yml ; https://github.com/cgat-developers/cgat-flow/pull/14
+* new way of activating conda environments ; https://github.com/cgat-developers/cgat-flow/pull/15