prepare for 0.14.0

docs/content/history.rst

@@ -2,14 +2,24 @@
 Release History
 #############################
 
-0.14.0 (Future)
+0.15.0 (Future)
 =======================================
-1. Leverage genotype likelihoods in tools (e.g., de_novo and mendelelian_violations) as a means to prioritize confident variants.
-2. Standardize the output from the built-in tools into a common, BED+ format.
-3. Update parsing for newer snpEff version
+1. Leverage genotype likelihoods in tools other than `mendel_errors` as a means to prioritize confident variants.
+2. Update parsing for snpEff >= 4.0
+3. Add an `is_splicing` column.
+4. Support for multi-generational families.
+5. Attempt to provide better backwards compatibility.
+6. Continue to improve performance.
+
+0.14.0 
+=======================================
+1. Standardized the output from the built-in tools into a common, BED+ format. Thanks to feedback from Jessica Chong and Daniel Gaston.
+2. Release of `mendel_errors` tool which also outputs the type of error and the probability (based on PL's)
+3. Improvements to the `load` tool when running on large compute clusters using PBS, SGE, SLURM, etc. Also provde a workaround for NFS locking issues. Many thanks to Ben Weisburd in Daniel Macarthur's lab.
 4. Improve preprocess script to support varscan, platypus (https://gist.github.com/brentp/4db670df147cbd5a2b32)
-5. Expose `mendelian_error` tool which also outputs the type of error and the probability (based on PL's)
-6. Performance improvement to tools (pre-compile evals)
+5. Performance improvements for many of the built-in tools (pre-compile evals)
+6. Bug fix for installation with sudo privileges.
+
 
 0.13.1 (2015-Apr-09)
 =======================================

requirements.txt

@@ -14,4 +14,4 @@ pandas>=0.11.0
 openpyxl>=1.6.1,<2.0.0
 scipy>=0.12.0
 Unidecode>=0.04.14
-gemini>=0.13.1
+gemini>=0.14.0

versioning/0.14.0/requirements_conda.txt

@@ -0,0 +1,35 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+bx-python=0.7.2=np18py27_1
+conda=3.5.5=py27_0
+cython=0.20.1=py27_0
+dateutil=2.1=py27_2
+ipython=2.1.0=py27_2
+jinja2=2.7.2=py27_0
+libsodium=0.4.5=0
+markupsafe=0.18=py27_0
+nose=1.3.3=py27_0
+numpy=1.8.1=py27_0
+openssl=1.0.1h=0
+pandas=0.14.0=np18py27_0
+pip=1.5.6=py27_0
+pycosat=0.6.1=py27_0
+pycrypto=2.6.1=py27_0
+pyparsing=2.0.1=py27_0
+pysam=0.8.0=py27_0
+python=2.7.8=0
+pytz=2014.4=py27_0
+pyyaml=3.11=py27_0
+pyzmq=14.3.0=py27_0
+readline=6.2=2
+requests=2.3.0=py27_0
+scipy=0.14.0=np18py27_0
+setuptools=3.6=py27_0
+six=1.7.3=py27_0
+sqlite=3.8.4.1=0
+system=5.8=1
+tk=8.5.15=0
+yaml=0.1.4=0
+zeromq=4.0.4=0
+zlib=1.2.7=0

versioning/0.14.0/requirements_pip.txt

@@ -0,0 +1,17 @@
+numpy==1.8.1
+pyparsing==1.5.7
+pysam==0.8.0
+cyvcf==0.1.14
+PyYAML==3.11
+pybedtools==0.6.6
+jinja2==2.7.3
+python-graph-core==1.8.2
+python-graph-dot==1.8.2
+bottle==0.12.7
+ipython-cluster-helper==0.3.0
+bx-python==0.7.1
+pandas==0.14.0
+openpyxl==1.8.6
+scipy==0.14.0
+Unidecode==0.04.16
+gemini>=0.14.0