Merge pull request #79 from RNAer/snakemake

use snakemake and IntervalMetadata
biocore · Nov 8, 2016 · 93d4db6 · 93d4db6
2 parents c1b688b + b5f6d8e
commit 93d4db6
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Showing 140 changed files with 947 additions and 30,930 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -14,6 +14,8 @@ before_install:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
+  - conda config --add channels conda-forge
+  - conda config --add channels https://conda.anaconda.org/bioconda
   - conda config --add channels https://conda.anaconda.org/zechxu
   # Update conda itself
   - conda update -q conda

diff --git a/Makefile b/Makefile
@@ -26,4 +26,4 @@ pep8:
 html:
 	make -C doc clean html
 
-all: pep8 html test
+all: test pep8 html
diff --git a/ci/conda_requirements.txt b/ci/conda_requirements.txt
@@ -1,10 +1,13 @@
-pip
 nose
 pep8
 flake8
+snakemake
 infernal
 hmmer
 prodigal
-diamond>=0.7.12
-scikit-bio=0.4.2dev
+diamond=0.8.22
+aragorn
+scikit-bio>=0.5
 minced
+sphinx
+click>=6.0
diff --git a/ci/pip_requirements.txt b/ci/pip_requirements.txt
@@ -1,4 +1 @@
-sphinx
-click>=6.0
 coveralls
-git+git://github.com/rnaer/dumpling.git
diff --git a/doc/bfillings.rst b/doc/bfillings.rst
diff --git a/micronota/__init__.py b/micronota/__init__.py
@@ -7,7 +7,7 @@
 # ----------------------------------------------------------------------------
 
 # import the parsers so they are available
-from .parsers import embl, sam  # noqa
+from .parsers import sam  # noqa
 
 
 __credits__ = "https://github.com/biocore/micronota/graphs/contributors"

diff --git a/micronota/bfillings/__init__.py b/micronota/bfillings/__init__.py
diff --git a/micronota/bfillings/_base.py b/micronota/bfillings/_base.py