From 52c8e0c0f71edd995e8c1055be50c7ade94758df Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 11:50:14 -0700 Subject: [PATCH 01/10] DO NOT MERGE --- .travis.yml | 9 ++++++--- replicate.sh | 7 +++++++ 2 files changed, 13 insertions(+), 3 deletions(-) create mode 100644 replicate.sh diff --git a/.travis.yml b/.travis.yml index 386fd6e..4f1e95e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,11 +12,14 @@ before_install: install: - 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 + - conda install --yes -c bioconda "VSEARCH=2.6.0" MAFFT=7.310 SortMeRNA=2.0 - pip install -U pip coveralls - pip install --process-dependency-links . script: - - 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 10 + - cat /proc/cpuinfo after_success: - coveralls 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 $(seq 1 10) +do + python deblur/test/test_workflow.py workflowTests.test_dereplicate_seqs +done From 670ccf03d4c67a25c78bed78ecc36646c676f4b7 Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 12:45:48 -0700 Subject: [PATCH 02/10] Kick --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 4f1e95e..03bc76c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,7 @@ before_install: install: - conda create --yes -n deblur python=$PYTHON_VERSION pip nose flake8 h5py - source activate deblur - - conda install --yes -c bioconda "VSEARCH=2.6.0" MAFFT=7.310 SortMeRNA=2.0 + - conda install --yes -c bioconda "VSEARCH=2.8.3" MAFFT=7.310 SortMeRNA=2.0 - pip install -U pip coveralls - pip install --process-dependency-links . script: From 82651ac89d88704012a0f029adc61b852911d9cc Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 12:58:53 -0700 Subject: [PATCH 03/10] Kick 2 --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 03bc76c..8ffdaf9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,5 +21,6 @@ script: - bash replicate.sh - dmesg | tail -n 10 - cat /proc/cpuinfo + - echo "kcik" after_success: - coveralls From 5e5aebbb5a85a4e34b30d35c791a323654257885 Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 13:18:14 -0700 Subject: [PATCH 04/10] MRE --- .travis.yml | 11 +++-------- seqs.fasta | 14 ++++++++++++++ 2 files changed, 17 insertions(+), 8 deletions(-) create mode 100644 seqs.fasta diff --git a/.travis.yml b/.travis.yml index 8ffdaf9..464ba9a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,17 +10,12 @@ 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=2.8.3" 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: - vsearch --version - ldd $(which vsearch) - - bash replicate.sh + - vsearch --derep_fulllength seqs.fasta --output seqs_derep.fasta --sizeout --fasta_width 0 --minuniquesize 1 --quiet --threads 1 - dmesg | tail -n 10 - cat /proc/cpuinfo - - echo "kcik" -after_success: - - coveralls 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 From 2c4504bd98112b4e8ea3570ed4215d79697f98b7 Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 13:28:13 -0700 Subject: [PATCH 05/10] MRE kick --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 464ba9a..e254c42 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,4 +18,4 @@ script: - 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 - - cat /proc/cpuinfo + - head -n 25 /proc/cpuinfo From 93dc252c7689f6d2f36001bb08e39667a758970d Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 13:32:33 -0700 Subject: [PATCH 06/10] MRE kick 2 --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index e254c42..ffaedce 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,3 +19,5 @@ script: - 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" + From decf6b86614283675dc5b8ed2ae804d4c5d0a76e Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 13:35:39 -0700 Subject: [PATCH 07/10] MRE kick 3 --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index ffaedce..f367c66 100644 --- a/.travis.yml +++ b/.travis.yml @@ -20,4 +20,5 @@ script: - dmesg | tail -n 10 - head -n 25 /proc/cpuinfo - echo "kick" + - echo "kick" From 5f288c9d4f945e341394e68a1835a6f771f1ed6d Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 15:48:23 -0700 Subject: [PATCH 08/10] MRE kick 4 --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index f367c66..1af3e9f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,4 +21,5 @@ script: - head -n 25 /proc/cpuinfo - echo "kick" - echo "kick" + - echo "kick" From 41e52554eb90709297b95e3d06002d1f983432c5 Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Fri, 14 Sep 2018 16:18:01 -0700 Subject: [PATCH 09/10] MRE kick 5, please stop going to AMD systems --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 1af3e9f..3934534 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,4 +22,5 @@ script: - echo "kick" - echo "kick" - echo "kick" + - echo "kick" From a17fd5deadc65d2622a0b2de55b62405ded60602 Mon Sep 17 00:00:00 2001 From: Daniel McDonald Date: Sun, 16 Sep 2018 11:25:57 -0700 Subject: [PATCH 10/10] MRE kick 6, please stop going to AMD systems --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 3934534..e7a9c7c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,4 +23,5 @@ script: - echo "kick" - echo "kick" - echo "kick" + - echo "kick"