Merge bd580a1 into 25ac7de

.travis.yml

@@ -1,21 +1,30 @@
 language: python
 env:
   - PYTHON_VERSION=3.5
+  - PYTHON_VERSION=3.6
 before_install:
   - wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda3/bin:$PATH
   # Update conda itself
   - conda update --yes conda
+  - export TMPDIR=/tmp/deblur-testing
+  - mkdir $TMPDIR
 install:
-  - conda create --yes -n deblur python=$PYTHON_VERSION pip nose flake8 h5py
+  - conda create --yes -n deblur python=$PYTHON_VERSION pip nose flake8 h5py libgcc # "numpy<1.14.0,>=1.9.2"
   - source activate deblur
-  - conda install --yes -c bioconda "VSEARCH>=2.0.3" MAFFT=7.310 SortMeRNA=2.0
+  - conda install --yes -c bioconda "VSEARCH<2.6.0" 
+  - conda install --yes -c bioconda MAFFT=7.310 
+  - conda install --yes -c bioconda SortMeRNA=2.0
   - pip install -U pip coveralls
   - pip install --process-dependency-links .
 script:
-  - nosetests --with-doctest --with-coverage
-  - flake8 --max-line-length=200 deblur scripts/deblur setup.py
+  #- nosetests --with-doctest --with-coverage --cover-package=deblur
+    # flake8 --max-line-length=200 deblur scripts/deblur setup.py
+  - vsearch --version
+  - ldd $(which vsearch)
+  - bash replicate.sh 
+  - dmesg | tail -n 100
 after_success:
   - coveralls

deblur/workflow.py

@@ -961,4 +961,9 @@ def _system_call(cmd, stdoutfilename=None):
     # This call blocks until the command is done
     stdout, stderr = proc.communicate()
     return_value = proc.returncode
+
+    print(cmd)
+    print(stdout)
+    print(stderr)
+    print(return_value)
     return stdout, stderr, return_value

replicate.sh

@@ -0,0 +1,17 @@
+set -x 
+set -e
+
+#conda create --yes -n deblur-hammer python=3.5 pip nose flake8 h5py libgcc # "numpy<1.14.0,>=1.9.2"
+# source activate deblur-hammer
+#conda install --yes -c bioconda "VSEARCH=2.8.3"
+#conda install --yes -c bioconda MAFFT=7.310
+#conda install --yes -c bioconda SortMeRNA=2.0
+#pip install -U pip coveralls
+#pip install --process-dependency-links .
+#vsearch --version
+#ldd $(which vsearch)
+
+for i in $(seq 1 10)
+do
+  python deblur/test/test_workflow.py workflowTests.test_dereplicate_seqs
+done