From a84cb09d61e90d9c3996f9d01dc7cf648366d127 Mon Sep 17 00:00:00 2001 From: Michael Lovci Date: Fri, 16 Jun 2017 16:13:19 -0700 Subject: [PATCH 1/6] Build conda env locally Add make directive to build conda environment locally. --- Makefile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 5590116..b53ce25 100644 --- a/Makefile +++ b/Makefile @@ -67,7 +67,10 @@ dist: clean python setup.py bdist_wheel ls -l dist -install: clean +environment: + -conda env create -f environment.yml + +install: environment clean python setup.py install N_JOBS = -1 From 2a92a86694773a61e71f9936c2c083abff6b8cb6 Mon Sep 17 00:00:00 2001 From: mlovci Date: Mon, 19 Jun 2017 17:31:44 -0700 Subject: [PATCH 2/6] Use conda env before doing things --- Makefile | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Makefile b/Makefile index b53ce25..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 @@ -71,27 +71,27 @@ environment: -conda env create -f environment.yml install: environment clean - python setup.py install + 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 From 7d64c21c54364725dae330a523c75a996e915927 Mon Sep 17 00:00:00 2001 From: mlovci Date: Mon, 19 Jun 2017 17:39:59 -0700 Subject: [PATCH 3/6] modify install instructions for lazy people --- README.rst | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.rst b/README.rst index 6d7af35..fed9a2d 100644 --- a/README.rst +++ b/README.rst @@ -46,6 +46,19 @@ Features Installation ============ +Quick install +------------- + +(requires anaconda) + +:: + + make install + + +Manual Install +-------------- + To install ``outrigger``, we recommend using the `Anaconda Python Distribution `__ and creating an environment. From f12caefdca0b13c0e64302d7d552d70126b8008f Mon Sep 17 00:00:00 2001 From: mlovci Date: Mon, 19 Jun 2017 17:42:53 -0700 Subject: [PATCH 4/6] Use make on travis --- .travis.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) 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" From c770f0e5259016a3567b9dfed3c2460123cfb823 Mon Sep 17 00:00:00 2001 From: mlovci Date: Mon, 19 Jun 2017 17:43:17 -0700 Subject: [PATCH 5/6] Clarify installation instructions --- README.rst | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index fed9a2d..5f2d489 100644 --- a/README.rst +++ b/README.rst @@ -46,21 +46,28 @@ Features Installation ============ +To install ``outrigger``, we recommend using the `Anaconda Python +Distribution `__ and creating an environment. + Quick install ------------- -(requires anaconda) +(Requires anaconda) :: make install +Then, activate the anaconda environment to put outrigger commands in your $PATH + +:: + + source activate outrigger-env + Manual Install -------------- -To install ``outrigger``, we recommend using the `Anaconda Python -Distribution `__ and creating an environment. You'll want to add the `bioconda `__ channel to make installing `bedtools `__ and @@ -86,6 +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: From b5e27d46d55110c6ef3f37f7285a4b36c9263527 Mon Sep 17 00:00:00 2001 From: mlovci Date: Mon, 19 Jun 2017 17:47:56 -0700 Subject: [PATCH 6/6] remove meta.yml (so as not to be confused with environment.yml) --- meta.yml | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 meta.yml 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