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UPDATE: propose update to blast #2

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UPDATE: propose update to blast #2

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fa59daf
UPDATE: propose update to blast
kevinkle Mar 11, 2018
13f5d36
EDIT: added a comment to trip travis
kevinkle Mar 11, 2018
3cbe34b
DEBUG: display which blast version if error
kevinkle Mar 11, 2018
07af52b
FIX: provide access to bioconda for blast update
kevinkle Mar 11, 2018
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38 changes: 38 additions & 0 deletions .travis.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
sudo: required
lanugage: python
python:
- "2.7"
before_install:
- sudo apt-get update
# Install miniconda.
- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
else
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
fi
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
install:
- conda create --name phylotyper
- source activate phylotyper
- conda install -c mdwhitesi -c bioconda -c conda-forge -c compbiocore phylotyper
- mkdir out
script:
- phylotyper genome stx1 out example_data/genome.fasta
- phylotyper genome stx2 out example_data/genome.fasta
- phylotyper genome eae out example_data/genome.fasta
after_failure:
# This should not trip after we've update the blast ver.
- conda env export | grep blast
- conda update -c bioconda -c conda-forge -y blast
- conda env export | grep blast
- phylotyper genome stx1 out example_data/genome.fasta
- phylotyper genome stx2 out example_data/genome.fasta
- phylotyper genome eae out example_data/genome.fasta
notifications:
email: false
14 changes: 7 additions & 7 deletions conda/phylotyper/meta.yaml
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Expand Up @@ -5,7 +5,7 @@ package:
source:
fn: master.zip
url: https://github.com/superphy/insilico-subtyping/archive/master.zip
# md5:
# md5:
# patches:
# List any patch files here
# - fix.patch
Expand All @@ -29,7 +29,7 @@ build:

requirements:
build:
- python
- python
- biopython
- rpy2 <=2.8
- setuptools
Expand All @@ -51,13 +51,13 @@ requirements:
- r-igraph
- bioconductor-biostrings
- mafft
- blast 2.6.0
- blast >= 2.6.0
- fasttree
- trimal
- trimal

run:
- python
- biopython
- python
- biopython
- rpy2 <=2.8
- setuptools
- pytest
Expand All @@ -78,7 +78,7 @@ requirements:
- r-igraph
- bioconductor-biostrings
- mafft
- blast
- blast >= 2.7.1
- fasttree
- trimal

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