diff --git a/.travis.yml b/.travis.yml
index edcec64..dfb85d1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -18,9 +18,7 @@ before_install:
- which -a curl
install:
-- conda env create --file testing/environment_no_python.yml python=2.7
-- source activate outrigger-env
-- pip install .
+- make install
before_script:
- git config --global user.email "olga.botvinnik@gmail.com"
diff --git a/Makefile b/Makefile
index 5590116..28a5df6 100644
--- a/Makefile
+++ b/Makefile
@@ -44,7 +44,7 @@ lint:
flake8 --exclude outrigger/external,doc outrigger
test: clean-pyc
- py.test outrigger
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && py.test outrigger
coverage: clean-pyc
coverage run --source outrigger --omit="*/test*" --module py.test
@@ -67,28 +67,31 @@ dist: clean
python setup.py bdist_wheel
ls -l dist
-install: clean
- python setup.py install
+environment:
+ -conda env create -f environment.yml
+
+install: environment clean
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && python setup.py install
N_JOBS = -1
tasic2016:
rm -rf tasic2016_outrigger_output
- outrigger index --sj-out-tab outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/*SJ.out.tab --gtf outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf --output tasic2016_outrigger_output --n-jobs $(N_JOBS)
- outrigger validate --genome ~/genomes/mm10/mm10.chrom.sizes --fasta ~/genomes/mm10/gencode/m10/GRCm38.primary_assembly.genome.fa --output tasic2016_outrigger_output
- outrigger psi --output tasic2016_outrigger_output --n-jobs $(N_JOBS)
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && outrigger index --sj-out-tab outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/*SJ.out.tab --gtf outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf --output tasic2016_outrigger_output --n-jobs $(N_JOBS)
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && outrigger validate --genome ~/genomes/mm10/mm10.chrom.sizes --fasta ~/genomes/mm10/gencode/m10/GRCm38.primary_assembly.genome.fa --output tasic2016_outrigger_output
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && outrigger psi --output tasic2016_outrigger_output --n-jobs $(N_JOBS)
treutlein2014: clean-output
rm -rf treutlein2014
- outrigger index \
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && outrigger index \
-j outrigger/tests/data/io/star/treutlein2014/sj_out_tab/* \
-g outrigger/tests/data/io/gtf/treutlein2014/gencode.vM2.annotation.fgfr2.gtf \
-o treutlein2014
arabdopsis: clean-output
- outrigger index \
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && outrigger index \
--sj-out-tab outrigger/tests/data/arabdopsis/unprocessed/rna.chr4.subset.SJ.out.tab \
--gtf outrigger/tests/data/arabdopsis/unprocessed/Arabidopsis_thaliana.TAIR10.31.chr4.subset.gtf \
--min-reads 1 --n-jobs $(N_JOBS) \
--output arabdopsis_outrigger_output
- outrigger psi --n-jobs $(N_JOBS) --output arabdopsis_outrigger_output
+ source activate `cat environment.yml |grep name | cut -f2 -d " "` && outrigger psi --n-jobs $(N_JOBS) --output arabdopsis_outrigger_output
diff --git a/README.rst b/README.rst
index 6d7af35..5f2d489 100644
--- a/README.rst
+++ b/README.rst
@@ -49,6 +49,26 @@ Installation
To install ``outrigger``, we recommend using the `Anaconda Python
Distribution `__ and creating an environment.
+Quick install
+-------------
+
+(Requires anaconda)
+
+::
+
+ make install
+
+Then, activate the anaconda environment to put outrigger commands in your $PATH
+
+::
+
+ source activate outrigger-env
+
+
+Manual Install
+--------------
+
+
You'll want to add the `bioconda `__
channel to make installing `bedtools `__ and
its Python wrapper, `pybedtools `__
@@ -73,6 +93,17 @@ Now activate that environment:
source activate outrigger-env
+
+And run the installation:
+
+::
+
+ pip install .
+
+
+Validate Installation
+---------------------
+
To check that it installed properly, try the command with the help
option (``-h``), ``outrigger -h``. The output should look like this:
diff --git a/meta.yml b/meta.yml
deleted file mode 100644
index 1751275..0000000
--- a/meta.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-
-package:
- name: outrigger
- version: 0.2.8
-
-source:
- path: .
-
-requirements:
- build:
- - python
- run:
- - python
- - pandas>=0.17.0
- - setuptools
- - gffutils
- - pybedtools
- - biopython
- - bedtools
- - joblib
-
-test:
- imports:
- - outrigger
-
-about:
- home: https://github.com/YeoLab/outrigger
- summary: Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
- license: BSD 3-Clause