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