diff --git a/.travis.yml b/.travis.yml index 386fd6e..e7a9c7c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,13 +10,18 @@ before_install: # Update conda itself - conda update --yes conda 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 - source activate deblur - - conda install --yes -c bioconda "VSEARCH=2.7.0" MAFFT=7.310 SortMeRNA=2.0 - - pip install -U pip coveralls - - pip install --process-dependency-links . + - conda install --yes -c bioconda "VSEARCH=2.8.3" #MAFFT=7.310 SortMeRNA=2.0 script: - - nosetests --with-doctest --with-coverage --cover-package=deblur - - flake8 --max-line-length=200 deblur scripts/deblur setup.py -after_success: - - coveralls + - vsearch --version + - ldd $(which vsearch) + - vsearch --derep_fulllength seqs.fasta --output seqs_derep.fasta --sizeout --fasta_width 0 --minuniquesize 1 --quiet --threads 1 + - dmesg | tail -n 10 + - head -n 25 /proc/cpuinfo + - echo "kick" + - echo "kick" + - echo "kick" + - echo "kick" + - echo "kick" + diff --git a/replicate.sh b/replicate.sh new file mode 100644 index 0000000..f8f7a59 --- /dev/null +++ b/replicate.sh @@ -0,0 +1,7 @@ +set -x +set -e + +for i in $(seq 1 10) +do + python deblur/test/test_workflow.py workflowTests.test_dereplicate_seqs +done diff --git a/seqs.fasta b/seqs.fasta new file mode 100644 index 0000000..810aa16 --- /dev/null +++ b/seqs.fasta @@ -0,0 +1,14 @@ +>seq1 +TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG +>seq2 +TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG +>seq3 +TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG +>seq4 +TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCT +>seq5 +TACCAGCCCCTTAAGTGGTAGGGACGATTATTTGGCCTAAAGCGTCCG +>seq6 +CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT +>seq7 +CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT