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| __version__ = "0.3.0" | ||
| __version__ = "0.3.1" |
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| ============= | ||
| Release notes | ||
| Release Notes | ||
| ============= | ||
|
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||
| The full CGAT code collection is unreleased. Please use | ||
| the latest version from the repository. | ||
| The code collection is under continuous improvement and the | ||
| latest code can always be found in the code repository. | ||
| Nevertheless, we occasionally prepare releases. Notes on | ||
| each release are below. | ||
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| Contributions | ||
| Release 0.3.1 | ||
| ============= | ||
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| We included publicly and freely available code into the tool | ||
| collection for convenience. | ||
| * bugfix cgat CLI | ||
| * added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh | ||
| * modified install script to use conda environment files instead of conda meta-packages; https://github.com/CGATOxford/cgat/pull/343 | ||
| * update test_style.py to reflect new repository structure; https://github.com/CGATOxford/cgat/pull/345 | ||
| * update test_import.py to reflect new repository structure; https://github.com/CGATOxford/cgat/commit/decc5ec0e93b4d2c05b6fa3793b5a73caf1fa8b9 | ||
| * added script to perform Gene Set Enrichment Analysis; https://github.com/CGATOxford/cgat/pull/344 | ||
| * updated scripts to work with Python 3.6; https://github.com/CGATOxford/cgat/pull/346 | ||
| * bugfix bed2bed script; https://github.com/CGATOxford/cgat/pull/349; https://github.com/CGATOxford/cgat/issues/347 | ||
| * bugfix GTF.py module file; https://github.com/CGATOxford/cgat/issues/350 | ||
| * various bugfixes for Python 3 problems when running pipeline_annotations in python 3, plus a modification of the new "assembly report" section to allow genomes without a standard assembly report (e.g. yeast) to be processed; https://github.com/CGATOxford/cgat/pull/348 | ||
| * refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; https://github.com/CGATOxford/cgat/pull/354 | ||
| * removed unused imports with autoflakes; https://github.com/CGATOxford/cgat/pull/355 | ||
| * removed basestr, use str instead in Python 3; https://github.com/CGATOxford/cgat/pull/359 | ||
| * added test for csv2db; https://github.com/CGATOxford/cgat/pull/360 | ||
| * fixed rename_transcripts test for gtf2gtf.py; https://github.com/CGATOxford/cgat/pull/361 | ||
| * updated installation; https://github.com/CGATOxford/cgat/pull/364 ; https://github.com/CGATOxford/cgat/pull/373 | ||
| * updated documentation; https://github.com/CGATOxford/cgat/pull/365 ; https://github.com/CGATOxford/cgat/pull/367 | ||
| * replaced bx.bbi.bigwig_file with pyBigWig ; https://github.com/CGATOxford/cgat/pull/369 | ||
| * updated Expression.py to iterate over pandas dataframe; https://github.com/CGATOxford/cgat/pull/370 | ||
| * updated Expression.py to work with DESeq2 > 1.16 ; https://github.com/CGATOxford/cgat/pull/371 | ||
| * moved bed_vs_bed.py to obsolete ; https://github.com/CGATOxford/cgat/pull/372 | ||
|
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||
| * 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 | ||
| Release 0.3.0 | ||
| ============= | ||
|
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||
| First release of the code working in Python 3 only. | ||
|
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||
| Release 0.2.7 | ||
| ============= | ||
|
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||
| This release is compatible with pysam-0.11.1 and is the last | ||
| version of the code compatible with Python 2.7. Next releases | ||
| will be in Python 3 only. | ||
|
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||
| Release 0.2.6 | ||
| ============= | ||
|
|
||
| This release is compatible with pysam-0.10.0 and it is also half | ||
| way through the upgrade to Python 3 compatible code. | ||
|
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||
| Release 0.2.5 | ||
| ============= | ||
|
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||
| Minor bugfix release to ensure compatibility with pysam >= 0.8.4 | ||
|
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||
| Release 0.2.4 | ||
| ============= | ||
|
|
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| Minor bugfix release to ensure compatibility with pysam 0.8.4 | ||
|
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||
| Release 0.2.3 | ||
| ============= | ||
|
|
||
| Minor release to ensure compatibility with pysam-0.8.1 | ||
|
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||
| Release 0.2.2 | ||
| ============= | ||
|
|
||
| We have reviewed the command line options in all of the CGAT | ||
| scripts and have changed them to make them more consistent | ||
| between tools and more informative on the command line. This | ||
| means that existing scripts that call CGAT tools need to be | ||
| updated. A table with all options used in scripts and how | ||
| they have or have not changed | ||
| `here <https://github.com/CGATOxford/cgat/blob/master/tests/option_list.tsv>`_. | ||
|
|
||
| There is a script called `cgat_refactor.py | ||
| <https://github.com/CGATOxford/cgat/blob/master/refactor/cgat_refactor.py>`_ | ||
| to facilicate refactoring the repository. Instructions on how to use | ||
| the script are given at the command line help. | ||
|
|
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| There are also several bugfixes and new features. | ||
|
|
||
| Release 0.2.1 | ||
| ============= | ||
|
|
||
| Bugfix release | ||
|
|
||
| * Fixed a variety of bugs | ||
| * Increased test coverage | ||
| * Updated documentation | ||
| * Added paired read counting to gtf2table | ||
|
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||
| Release 0.2 | ||
| =========== | ||
|
|
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| * release for CGAT manuscript - fixed various installation issues | ||
|
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||
| Release 0.1.9 | ||
| ============= | ||
|
|
||
| * alignlib incompatibility fixed | ||
| * various bugfixes | ||
|
|
||
| Release 0.1.8 | ||
| ============= | ||
|
|
||
| * OS X compatibility release | ||
| * various bugfixes | ||
|
|
||
| Contributors | ||
| ------------ | ||
|
|
||
| Andreas Heger | ||
| Antonio Berlanga-Taylor | ||
| Martin Dienstbier | ||
| Nicholas Ilott | ||
| Jethro Johnson | ||
| Katherine Fawcett | ||
| Stephen Sansom | ||
| David Sims | ||
| Ian Sudbery | ||
| Hu Xiaoming | ||
| ============ | ||
|
|
||
| The following people have contributed to the CGAT Code collection: | ||
|
|
||
| * Andreas Heger | ||
| * Antonio Berlanga-Taylor | ||
| * Martin Dienstbier | ||
| * Nicholas Ilott | ||
| * Jethro Johnson | ||
| * Katherine Fawcett | ||
| * Stephen Sansom | ||
| * David Sims | ||
| * Ian Sudbery | ||
| * Hu Xiaoming | ||
| * Lesheng Kong | ||
| * Michael Morgan | ||
| * Thomas Smith | ||
| * Katherine Brown | ||
| * Charlotte George | ||
| * Adam Cribbs | ||
| * Hania Pavlou | ||
| * Reshma Nibhani | ||
| * Sebastian Luna-Valero | ||
|
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||
| 3rd party code | ||
| ============== | ||
|
|
||
| The CGAT code collection has been made possible by the many developers | ||
| in the bioinformatics and python community that have made their code | ||
| available for sharing. The code collection includes some snippets of | ||
| code taken from elsewhere for convenience, most notably: | ||
|
|
||
| 1. IGV.py from Brent Petersen | ||
| https://github.com/brentp/bio-playground/blob/master/igv/igv.py | ||
|
|
||
| 2. Nested containment list from the Pygr project | ||
| http://code.google.com/p/pygr/ | ||
|
|
||
| 3. SVGdraw.py was written by Fedor Baart & Hans de Wit | ||
|
|
||
| 4. list_overlap.py from Brent Petersen | ||
| https://github.com/brentp/bio-playground/blob/master/utils/list_overlap_p.py | ||
|
|
||
| 5. Iterators.py from an unknown source. | ||
|
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||
| Licence | ||
| ======= | ||
|
|
||
| The CGAT code is released under the new BSD licence:: | ||
|
|
||
| Copyright (c) 2013, Andreas Heger, MRC CGAT | ||
|
|
||
| All rights reserved. | ||
|
|
||
| Redistribution and use in source and binary forms, with or without | ||
| modification, are permitted provided that the following conditions are | ||
| met: | ||
|
|
||
| Redistributions of source code must retain the above copyright | ||
| notice, this list of conditions and the following disclaimer. | ||
| Redistributions in binary form must reproduce the above copyright | ||
| notice, this list of conditions and the following disclaimer in | ||
| the documentation and/or other materials provided with the | ||
| distribution. Neither the name of the Medical Research Council nor the | ||
| names of its contributors may be used to endorse or promote | ||
| products derived from this software without specific prior written | ||
| permission. | ||
|
|
||
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS | ||
| "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT | ||
| LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | ||
| A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | ||
| HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, | ||
| SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT | ||
| LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | ||
| DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | ||
| THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
| (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
| OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
|
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