From fa59daf15c54a797ee14dbc6f86be3290b1ebce0 Mon Sep 17 00:00:00 2001
From: Kevin Le <kevin.kent.le@gmail.com>
Date: Sun, 11 Mar 2018 18:23:34 -0400
Subject: [PATCH 1/4] UPDATE: propose update to blast

---
 .travis.yml                | 35 +++++++++++++++++++++++++++++++++++
 conda/phylotyper/meta.yaml | 14 +++++++-------
 2 files changed, 42 insertions(+), 7 deletions(-)
 create mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..e9923f5
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,35 @@
+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:
+  - conda update -y 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
diff --git a/conda/phylotyper/meta.yaml b/conda/phylotyper/meta.yaml
index 9088c82..9a74e91 100644
--- a/conda/phylotyper/meta.yaml
+++ b/conda/phylotyper/meta.yaml
@@ -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
@@ -29,7 +29,7 @@ build:
 
 requirements:
   build:
-    - python 
+    - python
     - biopython
     - rpy2 <=2.8
     - setuptools
@@ -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
@@ -78,7 +78,7 @@ requirements:
     - r-igraph
     - bioconductor-biostrings
     - mafft
-    - blast
+    - blast >= 2.7.1
     - fasttree
     - trimal
 

From 13f5d36f45d6c75d8666359d22d45f317f1a84bb Mon Sep 17 00:00:00 2001
From: Kevin Le <kevin.kent.le@gmail.com>
Date: Sun, 11 Mar 2018 18:30:32 -0400
Subject: [PATCH 2/4] EDIT: added a comment to trip travis

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index e9923f5..206d760 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -27,6 +27,7 @@ script:
   - 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 update -y blast
   - phylotyper genome stx1 out example_data/genome.fasta
   - phylotyper genome stx2 out example_data/genome.fasta

From 3cbe34b81a294d3bea8e5321e11edca65e043d4b Mon Sep 17 00:00:00 2001
From: Kevin Le <kevin.kent.le@gmail.com>
Date: Sun, 11 Mar 2018 18:42:52 -0400
Subject: [PATCH 3/4] DEBUG: display which blast version if error

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 206d760..20a1026 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,7 +28,9 @@ script:
   - 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 -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

From 07af52bf68e0e21c8c3f9e9276a265cb56f97db0 Mon Sep 17 00:00:00 2001
From: Kevin Le <kevin.kent.le@gmail.com>
Date: Sun, 11 Mar 2018 18:46:00 -0400
Subject: [PATCH 4/4] FIX: provide access to bioconda for blast update

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 20a1026..a002e23 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -29,7 +29,7 @@ script:
 after_failure:
   # This should not trip after we've update the blast ver.
   - conda env export | grep blast
-  - conda update -y 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