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https://files.pythonhosted.org/packages/98/73/648ef8f161b8a284ff0c0b3f12c7844ddbbbc1f420665821a3b472d742d6/bcbio-nextgen-1.0.9.tar.gz#sha256=a0e047cf4e8e0e3d12d8af7208818e791ec3a2ed3c681a17731802c442b1bdf4 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.9 Found link https://files.pythonhosted.org/packages/3a/6b/6b36aeb84776855b491fc09e3c5fe5a6cfcf1473d6b5ef33d298551b434b/bcbio-nextgen-1.1.0.tar.gz#sha256=12c727aafcfdb8a034a3c2ab34f149c1d84c502a7e4558422fa0b77b46e7f533 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.0 Found link https://files.pythonhosted.org/packages/5e/fc/7e35d2e7666fefe730fb1a89a88e5764fc3857193d8448518a6220949494/bcbio-nextgen-1.1.1.tar.gz#sha256=756334f29c31d5bbf99014827b0bef8d9d3776dcfba8a7a780e8436adcde2fd5 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.1 Found link https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz#sha256=623e652147865507c1564e41e3c2106a07fc1fd830b0ecf0a389c120f203d5b5 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.2 Using version 1.1.2 (newest of versions: 1.1.2) Created temporary directory: /tmp/pip-unpack-906pa2fh Downloading https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz (2.4MB) Downloading from URL https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz#sha256=623e652147865507c1564e41e3c2106a07fc1fd830b0ecf0a389c120f203d5b5 (from https://pypi.org/simple/bcbio-nextgen/) Added bcbio-nextgen==1.1.2 from https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz#sha256=623e652147865507c1564e41e3c2106a07fc1fd830b0ecf0a389c120f203d5b5 to build tracker '/tmp/pip-req-tracker-95emwmxi' Running setup.py (path:/tmp/pip-wheel-rdvjr5gu/bcbio-nextgen/setup.py) egg_info for package bcbio-nextgen Running command python setup.py egg_info fatal: Not a git repository (or any of the parent directories): .git running egg_info creating pip-egg-info/bcbio_nextgen.egg-info writing top-level names to pip-egg-info/bcbio_nextgen.egg-info/top_level.txt writing pip-egg-info/bcbio_nextgen.egg-info/PKG-INFO writing dependency_links to pip-egg-info/bcbio_nextgen.egg-info/dependency_links.txt writing manifest file 'pip-egg-info/bcbio_nextgen.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/bcbio_nextgen.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'config/*.ini' writing manifest file 'pip-egg-info/bcbio_nextgen.egg-info/SOURCES.txt' Source in /tmp/pip-wheel-rdvjr5gu/bcbio-nextgen has version 1.1.2, which satisfies requirement bcbio-nextgen==1.1.2 from https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz#sha256=623e652147865507c1564e41e3c2106a07fc1fd830b0ecf0a389c120f203d5b5 Removed bcbio-nextgen==1.1.2 from https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz#sha256=623e652147865507c1564e41e3c2106a07fc1fd830b0ecf0a389c120f203d5b5 from build tracker '/tmp/pip-req-tracker-95emwmxi' Building wheels for collected packages: bcbio-nextgen Created temporary directory: /tmp/pip-wheel-htix8ble Running setup.py bdist_wheel for bcbio-nextgen: started Destination directory: /tmp/pip-wheel-htix8ble Running command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-wheel-rdvjr5gu/bcbio-nextgen/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-htix8ble fatal: Not a git repository (or any of the parent directories): .git running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/bcbio copying bcbio/setpath.py -> build/lib/bcbio copying bcbio/__init__.py -> build/lib/bcbio copying bcbio/utils.py -> build/lib/bcbio copying bcbio/install.py -> build/lib/bcbio creating build/lib/tests creating build/lib/tests/unit copying tests/unit/test_alignprep.py -> build/lib/tests/unit copying tests/unit/conftest.py -> build/lib/tests/unit copying tests/unit/data.py -> build/lib/tests/unit copying tests/unit/__init__.py -> build/lib/tests/unit creating build/lib/tests/integration copying tests/integration/test_S3_pipelines.py -> build/lib/tests/integration copying tests/integration/test_SequencingDump.py -> build/lib/tests/integration copying tests/integration/test_pipeline.py -> build/lib/tests/integration copying tests/integration/test_automated_analysis.py -> build/lib/tests/integration copying tests/integration/__init__.py -> build/lib/tests/integration creating build/lib/tests/unit/pipeline copying tests/unit/pipeline/__init__.py -> build/lib/tests/unit/pipeline copying tests/unit/pipeline/test_rnaseq.py -> build/lib/tests/unit/pipeline copying tests/unit/pipeline/test_datadict.py -> build/lib/tests/unit/pipeline creating build/lib/tests/unit/ngsalign copying tests/unit/ngsalign/__init__.py -> build/lib/tests/unit/ngsalign creating build/lib/tests/unit/distributed copying tests/unit/distributed/__init__.py -> build/lib/tests/unit/distributed copying tests/unit/distributed/test_transaction.py -> build/lib/tests/unit/distributed creating build/lib/tests/unit/upload copying tests/unit/upload/test_upload.py -> build/lib/tests/unit/upload copying tests/unit/upload/__init__.py -> build/lib/tests/unit/upload creating build/lib/tests/unit/rnaseq copying tests/unit/rnaseq/__init__.py -> build/lib/tests/unit/rnaseq copying tests/unit/rnaseq/test_ericscript.py -> build/lib/tests/unit/rnaseq creating build/lib/tests/integration/rnaseq copying tests/integration/rnaseq/__init__.py -> build/lib/tests/integration/rnaseq copying tests/integration/rnaseq/test_ericscript.py -> build/lib/tests/integration/rnaseq creating build/lib/bcbio/qc copying bcbio/qc/contamination.py -> build/lib/bcbio/qc copying bcbio/qc/qsignature.py -> build/lib/bcbio/qc copying bcbio/qc/atropos.py -> build/lib/bcbio/qc copying bcbio/qc/picard.py -> build/lib/bcbio/qc copying bcbio/qc/variant.py -> build/lib/bcbio/qc copying bcbio/qc/umi.py -> build/lib/bcbio/qc copying bcbio/qc/multiqc.py -> build/lib/bcbio/qc copying bcbio/qc/kraken.py -> build/lib/bcbio/qc copying bcbio/qc/preseq.py -> build/lib/bcbio/qc copying bcbio/qc/samtools.py -> build/lib/bcbio/qc copying bcbio/qc/qualimap.py -> build/lib/bcbio/qc copying bcbio/qc/chipseq.py -> build/lib/bcbio/qc copying bcbio/qc/__init__.py -> build/lib/bcbio/qc copying bcbio/qc/damage.py -> build/lib/bcbio/qc copying bcbio/qc/srna.py -> build/lib/bcbio/qc copying bcbio/qc/coverage.py -> build/lib/bcbio/qc copying bcbio/qc/viral.py -> build/lib/bcbio/qc copying bcbio/qc/fastqc.py -> build/lib/bcbio/qc creating build/lib/bcbio/hla copying bcbio/hla/bwakit.py -> build/lib/bcbio/hla copying bcbio/hla/groups.py -> build/lib/bcbio/hla copying bcbio/hla/__init__.py -> build/lib/bcbio/hla copying bcbio/hla/optitype.py -> build/lib/bcbio/hla creating build/lib/bcbio/server copying bcbio/server/background.py -> build/lib/bcbio/server copying bcbio/server/run.py -> build/lib/bcbio/server copying bcbio/server/__init__.py -> build/lib/bcbio/server copying bcbio/server/main.py -> build/lib/bcbio/server creating build/lib/bcbio/illumina copying bcbio/illumina/machine.py -> build/lib/bcbio/illumina copying bcbio/illumina/flowcell.py -> build/lib/bcbio/illumina copying bcbio/illumina/__init__.py -> build/lib/bcbio/illumina copying bcbio/illumina/samplesheet.py -> build/lib/bcbio/illumina copying bcbio/illumina/demultiplex.py -> build/lib/bcbio/illumina copying bcbio/illumina/transfer.py -> build/lib/bcbio/illumina creating build/lib/bcbio/pipeline copying bcbio/pipeline/sra.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/version.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/genome.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/tools.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/archive.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/variation.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/qcsummary.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/datadict.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/sample.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/run_info.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/fastq.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/alignment.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/shared.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/region.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/cleanbam.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/__init__.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/rnaseq.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/config_utils.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/main.py -> build/lib/bcbio/pipeline copying bcbio/pipeline/merge.py -> build/lib/bcbio/pipeline creating build/lib/bcbio/bed copying bcbio/bed/__init__.py -> build/lib/bcbio/bed creating build/lib/bcbio/cwl copying bcbio/cwl/tool.py -> build/lib/bcbio/cwl copying bcbio/cwl/defs.py -> build/lib/bcbio/cwl copying bcbio/cwl/hpc.py -> build/lib/bcbio/cwl copying bcbio/cwl/inspect.py -> build/lib/bcbio/cwl copying bcbio/cwl/cwlutils.py -> build/lib/bcbio/cwl copying bcbio/cwl/workflow.py -> build/lib/bcbio/cwl copying bcbio/cwl/create.py -> build/lib/bcbio/cwl copying bcbio/cwl/__init__.py -> build/lib/bcbio/cwl copying bcbio/cwl/main.py -> build/lib/bcbio/cwl creating build/lib/bcbio/provenance copying bcbio/provenance/do.py -> build/lib/bcbio/provenance copying bcbio/provenance/versioncheck.py -> build/lib/bcbio/provenance copying bcbio/provenance/diagnostics.py -> build/lib/bcbio/provenance copying bcbio/provenance/system.py -> build/lib/bcbio/provenance copying bcbio/provenance/profile.py -> build/lib/bcbio/provenance copying bcbio/provenance/data.py -> build/lib/bcbio/provenance copying bcbio/provenance/__init__.py -> build/lib/bcbio/provenance copying bcbio/provenance/programs.py -> build/lib/bcbio/provenance creating build/lib/bcbio/log copying bcbio/log/logbook_zmqpush.py -> build/lib/bcbio/log copying bcbio/log/__init__.py -> build/lib/bcbio/log creating build/lib/bcbio/hmmer copying bcbio/hmmer/search.py -> build/lib/bcbio/hmmer copying bcbio/hmmer/__init__.py -> build/lib/bcbio/hmmer creating build/lib/bcbio/workflow copying bcbio/workflow/stormseq.py -> build/lib/bcbio/workflow copying bcbio/workflow/xprize.py -> build/lib/bcbio/workflow copying bcbio/workflow/__init__.py -> build/lib/bcbio/workflow copying bcbio/workflow/template.py -> build/lib/bcbio/workflow creating build/lib/bcbio/structural copying bcbio/structural/validate.py -> build/lib/bcbio/structural copying bcbio/structural/battenberg.py -> build/lib/bcbio/structural copying bcbio/structural/regions.py -> build/lib/bcbio/structural copying bcbio/structural/cnvkit.py -> build/lib/bcbio/structural copying bcbio/structural/prioritize.py -> build/lib/bcbio/structural copying bcbio/structural/gatkcnv.py -> build/lib/bcbio/structural copying bcbio/structural/delly.py -> build/lib/bcbio/structural copying bcbio/structural/convert.py -> build/lib/bcbio/structural copying bcbio/structural/seq2c.py -> build/lib/bcbio/structural copying bcbio/structural/cn_mops.py -> build/lib/bcbio/structural copying bcbio/structural/purple.py -> build/lib/bcbio/structural copying bcbio/structural/titancna.py -> build/lib/bcbio/structural copying bcbio/structural/metasv.py -> build/lib/bcbio/structural copying bcbio/structural/pindel.py -> build/lib/bcbio/structural copying bcbio/structural/shared.py -> build/lib/bcbio/structural copying bcbio/structural/lumpy.py -> build/lib/bcbio/structural copying bcbio/structural/annotate.py -> build/lib/bcbio/structural copying bcbio/structural/plot.py -> build/lib/bcbio/structural copying bcbio/structural/wham.py -> build/lib/bcbio/structural copying bcbio/structural/__init__.py -> build/lib/bcbio/structural copying bcbio/structural/gridss.py -> build/lib/bcbio/structural copying bcbio/structural/purecn.py -> build/lib/bcbio/structural copying bcbio/structural/hydra.py -> build/lib/bcbio/structural copying bcbio/structural/manta.py -> build/lib/bcbio/structural creating build/lib/bcbio/bam copying bcbio/bam/callable.py -> build/lib/bcbio/bam copying bcbio/bam/fasta.py -> build/lib/bcbio/bam copying bcbio/bam/cram.py -> build/lib/bcbio/bam copying bcbio/bam/skewer.py -> build/lib/bcbio/bam copying bcbio/bam/trim.py -> build/lib/bcbio/bam copying bcbio/bam/fastq.py -> build/lib/bcbio/bam copying bcbio/bam/counts.py -> build/lib/bcbio/bam copying bcbio/bam/ref.py -> build/lib/bcbio/bam copying bcbio/bam/readstats.py -> build/lib/bcbio/bam copying bcbio/bam/__init__.py -> build/lib/bcbio/bam copying bcbio/bam/coverage.py -> build/lib/bcbio/bam creating build/lib/bcbio/ngsalign copying bcbio/ngsalign/bbmap.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/minimap2.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/rtg.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/bowtie.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/postalign.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/bwa.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/alignprep.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/star.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/hisat2.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/__init__.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/mosaik.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/bowtie2.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/snap.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/tophat.py -> build/lib/bcbio/ngsalign copying bcbio/ngsalign/novoalign.py -> build/lib/bcbio/ngsalign creating build/lib/bcbio/picard copying bcbio/picard/metrics.py -> build/lib/bcbio/picard copying bcbio/picard/__init__.py -> build/lib/bcbio/picard copying bcbio/picard/utils.py -> build/lib/bcbio/picard creating build/lib/bcbio/distributed copying bcbio/distributed/clusterk.py -> build/lib/bcbio/distributed copying bcbio/distributed/runfn.py -> build/lib/bcbio/distributed copying bcbio/distributed/objectstore.py -> build/lib/bcbio/distributed copying bcbio/distributed/ipython.py -> build/lib/bcbio/distributed copying bcbio/distributed/transaction.py -> build/lib/bcbio/distributed copying bcbio/distributed/ipythontasks.py -> build/lib/bcbio/distributed copying bcbio/distributed/resources.py -> build/lib/bcbio/distributed copying bcbio/distributed/prun.py -> build/lib/bcbio/distributed copying bcbio/distributed/multitasks.py -> build/lib/bcbio/distributed copying bcbio/distributed/split.py -> build/lib/bcbio/distributed copying bcbio/distributed/__init__.py -> build/lib/bcbio/distributed copying bcbio/distributed/multi.py -> build/lib/bcbio/distributed copying bcbio/distributed/clargs.py -> build/lib/bcbio/distributed creating build/lib/bcbio/galaxy copying bcbio/galaxy/loc.py -> build/lib/bcbio/galaxy copying bcbio/galaxy/__init__.py -> build/lib/bcbio/galaxy copying bcbio/galaxy/nglims.py -> build/lib/bcbio/galaxy copying bcbio/galaxy/api.py -> build/lib/bcbio/galaxy creating build/lib/bcbio/broad copying bcbio/broad/metrics.py -> build/lib/bcbio/broad copying bcbio/broad/picardrun.py -> build/lib/bcbio/broad copying bcbio/broad/__init__.py -> build/lib/bcbio/broad creating build/lib/bcbio/variation copying bcbio/variation/varscan.py -> build/lib/bcbio/variation copying bcbio/variation/naming.py -> build/lib/bcbio/variation copying bcbio/variation/validate.py -> build/lib/bcbio/variation copying bcbio/variation/prioritize.py -> build/lib/bcbio/variation copying bcbio/variation/effects.py -> build/lib/bcbio/variation copying bcbio/variation/mutect.py -> build/lib/bcbio/variation copying bcbio/variation/vardict.py -> build/lib/bcbio/variation copying bcbio/variation/platypus.py -> build/lib/bcbio/variation copying bcbio/variation/recalibrate.py -> build/lib/bcbio/variation copying bcbio/variation/population.py -> build/lib/bcbio/variation copying bcbio/variation/pisces.py -> build/lib/bcbio/variation copying bcbio/variation/vcfanno.py -> build/lib/bcbio/variation copying bcbio/variation/joint.py -> build/lib/bcbio/variation copying bcbio/variation/ensemble.py -> build/lib/bcbio/variation copying bcbio/variation/peddy.py -> build/lib/bcbio/variation copying bcbio/variation/vcfutils.py -> build/lib/bcbio/variation copying bcbio/variation/gatkjoint.py -> build/lib/bcbio/variation copying bcbio/variation/samtools.py -> build/lib/bcbio/variation copying bcbio/variation/bedutils.py -> build/lib/bcbio/variation copying bcbio/variation/mutect2.py -> build/lib/bcbio/variation copying bcbio/variation/realign.py -> build/lib/bcbio/variation copying bcbio/variation/smcounter2.py -> build/lib/bcbio/variation copying bcbio/variation/normalize.py -> build/lib/bcbio/variation copying bcbio/variation/qsnp.py -> build/lib/bcbio/variation copying bcbio/variation/split.py -> build/lib/bcbio/variation copying bcbio/variation/validateplot.py -> build/lib/bcbio/variation copying bcbio/variation/__init__.py -> build/lib/bcbio/variation copying bcbio/variation/multi.py -> build/lib/bcbio/variation copying bcbio/variation/sentieon.py -> build/lib/bcbio/variation copying bcbio/variation/bamprep.py -> build/lib/bcbio/variation copying bcbio/variation/freebayes.py -> build/lib/bcbio/variation copying bcbio/variation/damage.py -> build/lib/bcbio/variation copying bcbio/variation/cortex.py -> build/lib/bcbio/variation copying bcbio/variation/vfilter.py -> build/lib/bcbio/variation copying bcbio/variation/gatkfilter.py -> build/lib/bcbio/variation copying bcbio/variation/coverage.py -> build/lib/bcbio/variation copying bcbio/variation/deepvariant.py -> build/lib/bcbio/variation copying bcbio/variation/octopus.py -> build/lib/bcbio/variation copying bcbio/variation/germline.py -> build/lib/bcbio/variation copying bcbio/variation/ploidy.py -> build/lib/bcbio/variation copying bcbio/variation/scalpel.py -> build/lib/bcbio/variation copying bcbio/variation/gatk.py -> build/lib/bcbio/variation copying bcbio/variation/strelka2.py -> build/lib/bcbio/variation copying bcbio/variation/genotype.py -> build/lib/bcbio/variation copying bcbio/variation/annotation.py -> build/lib/bcbio/variation creating build/lib/bcbio/upload copying bcbio/upload/filesystem.py -> build/lib/bcbio/upload copying bcbio/upload/s3.py -> build/lib/bcbio/upload copying bcbio/upload/galaxy.py -> build/lib/bcbio/upload copying bcbio/upload/irods.py -> build/lib/bcbio/upload copying bcbio/upload/shared.py -> build/lib/bcbio/upload copying bcbio/upload/__init__.py -> build/lib/bcbio/upload creating build/lib/bcbio/heterogeneity copying bcbio/heterogeneity/chromhacks.py -> build/lib/bcbio/heterogeneity copying bcbio/heterogeneity/theta.py -> build/lib/bcbio/heterogeneity copying bcbio/heterogeneity/__init__.py -> build/lib/bcbio/heterogeneity copying bcbio/heterogeneity/bubbletree.py -> build/lib/bcbio/heterogeneity copying bcbio/heterogeneity/loh.py -> build/lib/bcbio/heterogeneity copying bcbio/heterogeneity/phylowgs.py -> build/lib/bcbio/heterogeneity creating build/lib/bcbio/rnaseq copying bcbio/rnaseq/cufflinks.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/rapmap.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/cpat.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/variation.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/rsem.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/sailfish.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/bcbiornaseq.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/pizzly.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/umi.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/stringtie.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/ericscript.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/kallisto.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/oncofuse.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/__init__.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/gtf.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/dexseq.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/salmon.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/express.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/count.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/annotate_gtf.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/qc.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/spikein.py -> build/lib/bcbio/rnaseq copying bcbio/rnaseq/featureCounts.py -> build/lib/bcbio/rnaseq creating build/lib/bcbio/chipseq copying bcbio/chipseq/peaks.py -> build/lib/bcbio/chipseq copying bcbio/chipseq/macs2.py -> build/lib/bcbio/chipseq copying bcbio/chipseq/__init__.py -> build/lib/bcbio/chipseq creating build/lib/bcbio/graph copying bcbio/graph/graph.py -> build/lib/bcbio/graph copying bcbio/graph/__init__.py -> build/lib/bcbio/graph copying bcbio/graph/collectl.py -> build/lib/bcbio/graph creating build/lib/bcbio/srna copying bcbio/srna/mirdeep.py -> build/lib/bcbio/srna copying bcbio/srna/sample.py -> build/lib/bcbio/srna copying bcbio/srna/group.py -> build/lib/bcbio/srna copying bcbio/srna/umis.py -> build/lib/bcbio/srna copying bcbio/srna/__init__.py -> build/lib/bcbio/srna copying bcbio/srna/mirge.py -> build/lib/bcbio/srna copying bcbio/srna/qc.py -> build/lib/bcbio/srna creating build/lib/bcbio/pipeline/disambiguate copying bcbio/pipeline/disambiguate/run.py -> build/lib/bcbio/pipeline/disambiguate copying bcbio/pipeline/disambiguate/__init__.py -> build/lib/bcbio/pipeline/disambiguate running egg_info writing bcbio_nextgen.egg-info/PKG-INFO writing dependency_links to bcbio_nextgen.egg-info/dependency_links.txt writing top-level names to bcbio_nextgen.egg-info/top_level.txt reading manifest file 'bcbio_nextgen.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'config/*.ini' writing manifest file 'bcbio_nextgen.egg-info/SOURCES.txt' creating build/lib/bcbio/data creating build/lib/bcbio/data/umis copying bcbio/data/umis/10x_v2-cb1.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/10x_v2-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/dropseq-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v2-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-indrop-v3-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-scrb-cb1.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/harvard-scrb-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/icell8-cb1.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/icell8-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/qiagen_smallRNA_umi-transform.json -> build/lib/bcbio/data/umis copying bcbio/data/umis/surecell-cb1.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/surecell-cb2.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/surecell-cb3.txt.gz -> build/lib/bcbio/data/umis copying bcbio/data/umis/surecell-transform.json -> build/lib/bcbio/data/umis running build_scripts creating build/scripts-3.4 copying and adjusting scripts/bcbio_nextgen.py -> build/scripts-3.4 copying and adjusting scripts/bcbio_setup_genome.py -> build/scripts-3.4 copying and adjusting scripts/bcbio_prepare_samples.py -> build/scripts-3.4 copying and adjusting scripts/bcbio_fastq_umi_prep.py -> build/scripts-3.4 copying and adjusting scripts/cwltool2wdl.py -> build/scripts-3.4 changing mode of build/scripts-3.4/bcbio_nextgen.py from 644 to 755 changing mode of build/scripts-3.4/bcbio_setup_genome.py from 644 to 755 changing mode of build/scripts-3.4/bcbio_prepare_samples.py from 644 to 755 changing mode of build/scripts-3.4/bcbio_fastq_umi_prep.py from 644 to 755 changing mode of build/scripts-3.4/cwltool2wdl.py from 644 to 755 installing to build/bdist.linux-armv7l/wheel running install running install_lib creating build/bdist.linux-armv7l creating build/bdist.linux-armv7l/wheel creating build/bdist.linux-armv7l/wheel/tests creating build/bdist.linux-armv7l/wheel/tests/unit creating build/bdist.linux-armv7l/wheel/tests/unit/pipeline copying build/lib/tests/unit/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/pipeline copying build/lib/tests/unit/pipeline/test_rnaseq.py -> build/bdist.linux-armv7l/wheel/tests/unit/pipeline copying build/lib/tests/unit/pipeline/test_datadict.py -> build/bdist.linux-armv7l/wheel/tests/unit/pipeline copying build/lib/tests/unit/test_alignprep.py -> build/bdist.linux-armv7l/wheel/tests/unit copying build/lib/tests/unit/conftest.py -> build/bdist.linux-armv7l/wheel/tests/unit copying build/lib/tests/unit/data.py -> build/bdist.linux-armv7l/wheel/tests/unit creating build/bdist.linux-armv7l/wheel/tests/unit/ngsalign copying build/lib/tests/unit/ngsalign/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/ngsalign creating build/bdist.linux-armv7l/wheel/tests/unit/distributed copying build/lib/tests/unit/distributed/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/distributed copying build/lib/tests/unit/distributed/test_transaction.py -> build/bdist.linux-armv7l/wheel/tests/unit/distributed copying build/lib/tests/unit/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit creating build/bdist.linux-armv7l/wheel/tests/unit/upload copying build/lib/tests/unit/upload/test_upload.py -> build/bdist.linux-armv7l/wheel/tests/unit/upload copying build/lib/tests/unit/upload/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/upload creating build/bdist.linux-armv7l/wheel/tests/unit/rnaseq copying build/lib/tests/unit/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/rnaseq copying build/lib/tests/unit/rnaseq/test_ericscript.py -> build/bdist.linux-armv7l/wheel/tests/unit/rnaseq creating build/bdist.linux-armv7l/wheel/tests/integration copying build/lib/tests/integration/test_S3_pipelines.py -> build/bdist.linux-armv7l/wheel/tests/integration copying build/lib/tests/integration/test_SequencingDump.py -> build/bdist.linux-armv7l/wheel/tests/integration copying build/lib/tests/integration/test_pipeline.py -> build/bdist.linux-armv7l/wheel/tests/integration copying build/lib/tests/integration/test_automated_analysis.py -> build/bdist.linux-armv7l/wheel/tests/integration copying build/lib/tests/integration/__init__.py -> build/bdist.linux-armv7l/wheel/tests/integration creating build/bdist.linux-armv7l/wheel/tests/integration/rnaseq copying build/lib/tests/integration/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/tests/integration/rnaseq copying build/lib/tests/integration/rnaseq/test_ericscript.py -> build/bdist.linux-armv7l/wheel/tests/integration/rnaseq creating build/bdist.linux-armv7l/wheel/bcbio creating build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/contamination.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/qsignature.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/atropos.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/picard.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/variant.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/umi.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/multiqc.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/kraken.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/preseq.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/samtools.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/qualimap.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/chipseq.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/damage.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/srna.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/coverage.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/viral.py -> build/bdist.linux-armv7l/wheel/bcbio/qc copying build/lib/bcbio/qc/fastqc.py -> build/bdist.linux-armv7l/wheel/bcbio/qc creating build/bdist.linux-armv7l/wheel/bcbio/hla copying build/lib/bcbio/hla/bwakit.py -> build/bdist.linux-armv7l/wheel/bcbio/hla copying build/lib/bcbio/hla/groups.py -> build/bdist.linux-armv7l/wheel/bcbio/hla copying build/lib/bcbio/hla/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/hla copying build/lib/bcbio/hla/optitype.py -> build/bdist.linux-armv7l/wheel/bcbio/hla creating build/bdist.linux-armv7l/wheel/bcbio/server copying build/lib/bcbio/server/background.py -> build/bdist.linux-armv7l/wheel/bcbio/server copying build/lib/bcbio/server/run.py -> build/bdist.linux-armv7l/wheel/bcbio/server copying build/lib/bcbio/server/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/server copying build/lib/bcbio/server/main.py -> build/bdist.linux-armv7l/wheel/bcbio/server creating build/bdist.linux-armv7l/wheel/bcbio/illumina copying build/lib/bcbio/illumina/machine.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina copying build/lib/bcbio/illumina/flowcell.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina copying build/lib/bcbio/illumina/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina copying build/lib/bcbio/illumina/samplesheet.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina copying build/lib/bcbio/illumina/demultiplex.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina copying build/lib/bcbio/illumina/transfer.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina creating build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/sra.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/version.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/genome.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/tools.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/archive.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/variation.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/qcsummary.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/datadict.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/sample.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/run_info.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/fastq.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/alignment.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/shared.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/region.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/cleanbam.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/rnaseq.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/config_utils.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline copying build/lib/bcbio/pipeline/main.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline creating build/bdist.linux-armv7l/wheel/bcbio/pipeline/disambiguate copying build/lib/bcbio/pipeline/disambiguate/run.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline/disambiguate copying build/lib/bcbio/pipeline/disambiguate/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline/disambiguate copying build/lib/bcbio/pipeline/merge.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline creating build/bdist.linux-armv7l/wheel/bcbio/bed copying build/lib/bcbio/bed/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/bed creating build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/tool.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/defs.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/hpc.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/inspect.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/cwlutils.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/workflow.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/create.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl copying build/lib/bcbio/cwl/main.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl creating build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/do.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/versioncheck.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/diagnostics.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/system.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/profile.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/data.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance copying build/lib/bcbio/provenance/programs.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance creating build/bdist.linux-armv7l/wheel/bcbio/log copying build/lib/bcbio/log/logbook_zmqpush.py -> build/bdist.linux-armv7l/wheel/bcbio/log copying build/lib/bcbio/log/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/log creating build/bdist.linux-armv7l/wheel/bcbio/hmmer copying build/lib/bcbio/hmmer/search.py -> build/bdist.linux-armv7l/wheel/bcbio/hmmer copying build/lib/bcbio/hmmer/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/hmmer creating build/bdist.linux-armv7l/wheel/bcbio/workflow copying build/lib/bcbio/workflow/stormseq.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow copying build/lib/bcbio/workflow/xprize.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow copying build/lib/bcbio/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow copying build/lib/bcbio/workflow/template.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow creating build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/validate.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/battenberg.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/regions.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/cnvkit.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/prioritize.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/gatkcnv.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/delly.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/convert.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/seq2c.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/cn_mops.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/purple.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/titancna.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/metasv.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/pindel.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/shared.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/lumpy.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/annotate.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/plot.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/wham.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/gridss.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/purecn.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/hydra.py -> build/bdist.linux-armv7l/wheel/bcbio/structural copying build/lib/bcbio/structural/manta.py -> build/bdist.linux-armv7l/wheel/bcbio/structural creating build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/callable.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/fasta.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/cram.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/skewer.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/trim.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/fastq.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/counts.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/ref.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/readstats.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/bam copying build/lib/bcbio/bam/coverage.py -> build/bdist.linux-armv7l/wheel/bcbio/bam creating build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bbmap.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/minimap2.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/rtg.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bowtie.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/postalign.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bwa.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/alignprep.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/star.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/hisat2.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/mosaik.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bowtie2.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/snap.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/tophat.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign copying build/lib/bcbio/ngsalign/novoalign.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign creating build/bdist.linux-armv7l/wheel/bcbio/picard copying build/lib/bcbio/picard/metrics.py -> build/bdist.linux-armv7l/wheel/bcbio/picard copying build/lib/bcbio/picard/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/picard copying build/lib/bcbio/picard/utils.py -> build/bdist.linux-armv7l/wheel/bcbio/picard copying build/lib/bcbio/setpath.py -> build/bdist.linux-armv7l/wheel/bcbio creating build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/clusterk.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/runfn.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/objectstore.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/ipython.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/transaction.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/ipythontasks.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/resources.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/prun.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/multitasks.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/split.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/multi.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed copying build/lib/bcbio/distributed/clargs.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed creating build/bdist.linux-armv7l/wheel/bcbio/galaxy copying build/lib/bcbio/galaxy/loc.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy copying build/lib/bcbio/galaxy/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy copying build/lib/bcbio/galaxy/nglims.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy copying build/lib/bcbio/galaxy/api.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy copying build/lib/bcbio/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio creating build/bdist.linux-armv7l/wheel/bcbio/broad copying build/lib/bcbio/broad/metrics.py -> build/bdist.linux-armv7l/wheel/bcbio/broad copying build/lib/bcbio/broad/picardrun.py -> build/bdist.linux-armv7l/wheel/bcbio/broad copying build/lib/bcbio/broad/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/broad creating build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/varscan.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/naming.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/validate.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/prioritize.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/effects.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/mutect.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/vardict.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/platypus.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/recalibrate.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/population.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/pisces.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/vcfanno.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/joint.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/ensemble.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/peddy.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/vcfutils.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/gatkjoint.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/samtools.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/bedutils.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/mutect2.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/realign.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/smcounter2.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/normalize.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/qsnp.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/split.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/validateplot.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/multi.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/sentieon.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/bamprep.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/freebayes.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/damage.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/cortex.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/vfilter.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/gatkfilter.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/coverage.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/deepvariant.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/octopus.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/germline.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/ploidy.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/scalpel.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/gatk.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/strelka2.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/genotype.py -> build/bdist.linux-armv7l/wheel/bcbio/variation copying build/lib/bcbio/variation/annotation.py -> build/bdist.linux-armv7l/wheel/bcbio/variation creating build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/upload/filesystem.py -> build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/upload/s3.py -> build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/upload/galaxy.py -> build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/upload/irods.py -> build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/upload/shared.py -> build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/upload/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/upload copying build/lib/bcbio/utils.py -> build/bdist.linux-armv7l/wheel/bcbio creating build/bdist.linux-armv7l/wheel/bcbio/heterogeneity copying build/lib/bcbio/heterogeneity/chromhacks.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity copying build/lib/bcbio/heterogeneity/theta.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity copying build/lib/bcbio/heterogeneity/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity copying build/lib/bcbio/heterogeneity/bubbletree.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity copying build/lib/bcbio/heterogeneity/loh.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity copying build/lib/bcbio/heterogeneity/phylowgs.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity creating build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/cufflinks.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/rapmap.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/cpat.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/variation.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/rsem.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/sailfish.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/bcbiornaseq.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/pizzly.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/umi.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/stringtie.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/ericscript.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/kallisto.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/oncofuse.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/gtf.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/dexseq.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/salmon.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/express.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/count.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/annotate_gtf.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/qc.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/spikein.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq copying build/lib/bcbio/rnaseq/featureCounts.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq creating build/bdist.linux-armv7l/wheel/bcbio/chipseq copying build/lib/bcbio/chipseq/peaks.py -> build/bdist.linux-armv7l/wheel/bcbio/chipseq copying build/lib/bcbio/chipseq/macs2.py -> build/bdist.linux-armv7l/wheel/bcbio/chipseq copying build/lib/bcbio/chipseq/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/chipseq copying build/lib/bcbio/install.py -> build/bdist.linux-armv7l/wheel/bcbio creating build/bdist.linux-armv7l/wheel/bcbio/graph copying build/lib/bcbio/graph/graph.py -> build/bdist.linux-armv7l/wheel/bcbio/graph copying build/lib/bcbio/graph/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/graph copying build/lib/bcbio/graph/collectl.py -> build/bdist.linux-armv7l/wheel/bcbio/graph creating build/bdist.linux-armv7l/wheel/bcbio/data creating build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v2-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/qiagen_smallRNA_umi-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/icell8-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/surecell-cb2.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/icell8-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/dropseq-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-scrb-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/surecell-cb3.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/surecell-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/10x_v2-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/surecell-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-scrb-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/10x_v2-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis copying build/lib/bcbio/data/umis/harvard-indrop-v3-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis creating build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/mirdeep.py -> build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/sample.py -> build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/group.py -> build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/umis.py -> build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/mirge.py -> build/bdist.linux-armv7l/wheel/bcbio/srna copying build/lib/bcbio/srna/qc.py -> build/bdist.linux-armv7l/wheel/bcbio/srna running install_egg_info Copying bcbio_nextgen.egg-info to build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2-py3.4.egg-info running install_scripts creating build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data creating build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts copying build/scripts-3.4/bcbio_prepare_samples.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts copying build/scripts-3.4/bcbio_nextgen.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts copying build/scripts-3.4/bcbio_setup_genome.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts copying build/scripts-3.4/cwltool2wdl.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts copying build/scripts-3.4/bcbio_fastq_umi_prep.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts/bcbio_prepare_samples.py to 755 changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts/bcbio_nextgen.py to 755 changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts/bcbio_setup_genome.py to 755 changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts/cwltool2wdl.py to 755 changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.data/scripts/bcbio_fastq_umi_prep.py to 755 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") creating build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.2.dist-info/WHEEL creating '/tmp/pip-wheel-htix8ble/bcbio_nextgen-1.1.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it adding 'bcbio/__init__.py' adding 'bcbio/install.py' adding 'bcbio/setpath.py' adding 'bcbio/utils.py' adding 'bcbio/bam/__init__.py' adding 'bcbio/bam/callable.py' adding 'bcbio/bam/counts.py' adding 'bcbio/bam/coverage.py' adding 'bcbio/bam/cram.py' adding 'bcbio/bam/fasta.py' adding 'bcbio/bam/fastq.py' adding 'bcbio/bam/readstats.py' adding 'bcbio/bam/ref.py' adding 'bcbio/bam/skewer.py' adding 'bcbio/bam/trim.py' adding 'bcbio/bed/__init__.py' adding 'bcbio/broad/__init__.py' adding 'bcbio/broad/metrics.py' adding 'bcbio/broad/picardrun.py' adding 'bcbio/chipseq/__init__.py' adding 'bcbio/chipseq/macs2.py' adding 'bcbio/chipseq/peaks.py' adding 'bcbio/cwl/__init__.py' adding 'bcbio/cwl/create.py' adding 'bcbio/cwl/cwlutils.py' adding 'bcbio/cwl/defs.py' adding 'bcbio/cwl/hpc.py' adding 'bcbio/cwl/inspect.py' adding 'bcbio/cwl/main.py' adding 'bcbio/cwl/tool.py' adding 'bcbio/cwl/workflow.py' adding 'bcbio/data/umis/10x_v2-cb1.txt.gz' adding 'bcbio/data/umis/10x_v2-transform.json' adding 'bcbio/data/umis/dropseq-transform.json' adding 'bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz' adding 'bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz' adding 'bcbio/data/umis/harvard-indrop-v2-transform.json' adding 'bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz' adding 'bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz' adding 'bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz' adding 'bcbio/data/umis/harvard-indrop-v3-transform.json' adding 'bcbio/data/umis/harvard-scrb-cb1.txt.gz' adding 'bcbio/data/umis/harvard-scrb-transform.json' adding 'bcbio/data/umis/icell8-cb1.txt.gz' adding 'bcbio/data/umis/icell8-transform.json' adding 'bcbio/data/umis/qiagen_smallRNA_umi-transform.json' adding 'bcbio/data/umis/surecell-cb1.txt.gz' adding 'bcbio/data/umis/surecell-cb2.txt.gz' adding 'bcbio/data/umis/surecell-cb3.txt.gz' adding 'bcbio/data/umis/surecell-transform.json' adding 'bcbio/distributed/__init__.py' adding 'bcbio/distributed/clargs.py' adding 'bcbio/distributed/clusterk.py' adding 'bcbio/distributed/ipython.py' adding 'bcbio/distributed/ipythontasks.py' adding 'bcbio/distributed/multi.py' adding 'bcbio/distributed/multitasks.py' adding 'bcbio/distributed/objectstore.py' adding 'bcbio/distributed/prun.py' adding 'bcbio/distributed/resources.py' adding 'bcbio/distributed/runfn.py' adding 'bcbio/distributed/split.py' adding 'bcbio/distributed/transaction.py' adding 'bcbio/galaxy/__init__.py' adding 'bcbio/galaxy/api.py' adding 'bcbio/galaxy/loc.py' adding 'bcbio/galaxy/nglims.py' adding 'bcbio/graph/__init__.py' adding 'bcbio/graph/collectl.py' adding 'bcbio/graph/graph.py' adding 'bcbio/heterogeneity/__init__.py' adding 'bcbio/heterogeneity/bubbletree.py' adding 'bcbio/heterogeneity/chromhacks.py' adding 'bcbio/heterogeneity/loh.py' adding 'bcbio/heterogeneity/phylowgs.py' adding 'bcbio/heterogeneity/theta.py' adding 'bcbio/hla/__init__.py' adding 'bcbio/hla/bwakit.py' adding 'bcbio/hla/groups.py' adding 'bcbio/hla/optitype.py' adding 'bcbio/hmmer/__init__.py' adding 'bcbio/hmmer/search.py' adding 'bcbio/illumina/__init__.py' adding 'bcbio/illumina/demultiplex.py' adding 'bcbio/illumina/flowcell.py' adding 'bcbio/illumina/machine.py' adding 'bcbio/illumina/samplesheet.py' adding 'bcbio/illumina/transfer.py' adding 'bcbio/log/__init__.py' adding 'bcbio/log/logbook_zmqpush.py' adding 'bcbio/ngsalign/__init__.py' adding 'bcbio/ngsalign/alignprep.py' adding 'bcbio/ngsalign/bbmap.py' adding 'bcbio/ngsalign/bowtie.py' adding 'bcbio/ngsalign/bowtie2.py' adding 'bcbio/ngsalign/bwa.py' adding 'bcbio/ngsalign/hisat2.py' adding 'bcbio/ngsalign/minimap2.py' adding 'bcbio/ngsalign/mosaik.py' adding 'bcbio/ngsalign/novoalign.py' adding 'bcbio/ngsalign/postalign.py' adding 'bcbio/ngsalign/rtg.py' adding 'bcbio/ngsalign/snap.py' adding 'bcbio/ngsalign/star.py' adding 'bcbio/ngsalign/tophat.py' adding 'bcbio/picard/__init__.py' adding 'bcbio/picard/metrics.py' adding 'bcbio/picard/utils.py' adding 'bcbio/pipeline/__init__.py' adding 'bcbio/pipeline/alignment.py' adding 'bcbio/pipeline/archive.py' adding 'bcbio/pipeline/cleanbam.py' adding 'bcbio/pipeline/config_utils.py' adding 'bcbio/pipeline/datadict.py' adding 'bcbio/pipeline/fastq.py' adding 'bcbio/pipeline/genome.py' adding 'bcbio/pipeline/main.py' adding 'bcbio/pipeline/merge.py' adding 'bcbio/pipeline/qcsummary.py' adding 'bcbio/pipeline/region.py' adding 'bcbio/pipeline/rnaseq.py' adding 'bcbio/pipeline/run_info.py' adding 'bcbio/pipeline/sample.py' adding 'bcbio/pipeline/shared.py' adding 'bcbio/pipeline/sra.py' adding 'bcbio/pipeline/tools.py' adding 'bcbio/pipeline/variation.py' adding 'bcbio/pipeline/version.py' adding 'bcbio/pipeline/disambiguate/__init__.py' adding 'bcbio/pipeline/disambiguate/run.py' adding 'bcbio/provenance/__init__.py' adding 'bcbio/provenance/data.py' adding 'bcbio/provenance/diagnostics.py' adding 'bcbio/provenance/do.py' adding 'bcbio/provenance/profile.py' adding 'bcbio/provenance/programs.py' adding 'bcbio/provenance/system.py' adding 'bcbio/provenance/versioncheck.py' adding 'bcbio/qc/__init__.py' adding 'bcbio/qc/atropos.py' adding 'bcbio/qc/chipseq.py' adding 'bcbio/qc/contamination.py' adding 'bcbio/qc/coverage.py' adding 'bcbio/qc/damage.py' adding 'bcbio/qc/fastqc.py' adding 'bcbio/qc/kraken.py' adding 'bcbio/qc/multiqc.py' adding 'bcbio/qc/picard.py' adding 'bcbio/qc/preseq.py' adding 'bcbio/qc/qsignature.py' adding 'bcbio/qc/qualimap.py' adding 'bcbio/qc/samtools.py' adding 'bcbio/qc/srna.py' adding 'bcbio/qc/umi.py' adding 'bcbio/qc/variant.py' adding 'bcbio/qc/viral.py' adding 'bcbio/rnaseq/__init__.py' adding 'bcbio/rnaseq/annotate_gtf.py' adding 'bcbio/rnaseq/bcbiornaseq.py' adding 'bcbio/rnaseq/count.py' adding 'bcbio/rnaseq/cpat.py' adding 'bcbio/rnaseq/cufflinks.py' adding 'bcbio/rnaseq/dexseq.py' adding 'bcbio/rnaseq/ericscript.py' adding 'bcbio/rnaseq/express.py' adding 'bcbio/rnaseq/featureCounts.py' adding 'bcbio/rnaseq/gtf.py' adding 'bcbio/rnaseq/kallisto.py' adding 'bcbio/rnaseq/oncofuse.py' adding 'bcbio/rnaseq/pizzly.py' adding 'bcbio/rnaseq/qc.py' adding 'bcbio/rnaseq/rapmap.py' adding 'bcbio/rnaseq/rsem.py' adding 'bcbio/rnaseq/sailfish.py' adding 'bcbio/rnaseq/salmon.py' adding 'bcbio/rnaseq/spikein.py' adding 'bcbio/rnaseq/stringtie.py' adding 'bcbio/rnaseq/umi.py' adding 'bcbio/rnaseq/variation.py' adding 'bcbio/server/__init__.py' adding 'bcbio/server/background.py' adding 'bcbio/server/main.py' adding 'bcbio/server/run.py' adding 'bcbio/srna/__init__.py' adding 'bcbio/srna/group.py' adding 'bcbio/srna/mirdeep.py' adding 'bcbio/srna/mirge.py' adding 'bcbio/srna/qc.py' adding 'bcbio/srna/sample.py' adding 'bcbio/srna/umis.py' adding 'bcbio/structural/__init__.py' adding 'bcbio/structural/annotate.py' adding 'bcbio/structural/battenberg.py' adding 'bcbio/structural/cn_mops.py' adding 'bcbio/structural/cnvkit.py' adding 'bcbio/structural/convert.py' adding 'bcbio/structural/delly.py' adding 'bcbio/structural/gatkcnv.py' adding 'bcbio/structural/gridss.py' adding 'bcbio/structural/hydra.py' adding 'bcbio/structural/lumpy.py' adding 'bcbio/structural/manta.py' adding 'bcbio/structural/metasv.py' adding 'bcbio/structural/pindel.py' adding 'bcbio/structural/plot.py' adding 'bcbio/structural/prioritize.py' adding 'bcbio/structural/purecn.py' adding 'bcbio/structural/purple.py' adding 'bcbio/structural/regions.py' adding 'bcbio/structural/seq2c.py' adding 'bcbio/structural/shared.py' adding 'bcbio/structural/titancna.py' adding 'bcbio/structural/validate.py' adding 'bcbio/structural/wham.py' adding 'bcbio/upload/__init__.py' adding 'bcbio/upload/filesystem.py' adding 'bcbio/upload/galaxy.py' adding 'bcbio/upload/irods.py' adding 'bcbio/upload/s3.py' adding 'bcbio/upload/shared.py' adding 'bcbio/variation/__init__.py' adding 'bcbio/variation/annotation.py' adding 'bcbio/variation/bamprep.py' adding 'bcbio/variation/bedutils.py' adding 'bcbio/variation/cortex.py' adding 'bcbio/variation/coverage.py' adding 'bcbio/variation/damage.py' adding 'bcbio/variation/deepvariant.py' adding 'bcbio/variation/effects.py' adding 'bcbio/variation/ensemble.py' adding 'bcbio/variation/freebayes.py' adding 'bcbio/variation/gatk.py' adding 'bcbio/variation/gatkfilter.py' adding 'bcbio/variation/gatkjoint.py' adding 'bcbio/variation/genotype.py' adding 'bcbio/variation/germline.py' adding 'bcbio/variation/joint.py' adding 'bcbio/variation/multi.py' adding 'bcbio/variation/mutect.py' adding 'bcbio/variation/mutect2.py' adding 'bcbio/variation/naming.py' adding 'bcbio/variation/normalize.py' adding 'bcbio/variation/octopus.py' adding 'bcbio/variation/peddy.py' adding 'bcbio/variation/pisces.py' adding 'bcbio/variation/platypus.py' adding 'bcbio/variation/ploidy.py' adding 'bcbio/variation/population.py' adding 'bcbio/variation/prioritize.py' adding 'bcbio/variation/qsnp.py' adding 'bcbio/variation/realign.py' adding 'bcbio/variation/recalibrate.py' adding 'bcbio/variation/samtools.py' adding 'bcbio/variation/scalpel.py' adding 'bcbio/variation/sentieon.py' adding 'bcbio/variation/smcounter2.py' adding 'bcbio/variation/split.py' adding 'bcbio/variation/strelka2.py' adding 'bcbio/variation/validate.py' adding 'bcbio/variation/validateplot.py' adding 'bcbio/variation/vardict.py' adding 'bcbio/variation/varscan.py' adding 'bcbio/variation/vcfanno.py' adding 'bcbio/variation/vcfutils.py' adding 'bcbio/variation/vfilter.py' adding 'bcbio/workflow/__init__.py' adding 'bcbio/workflow/stormseq.py' adding 'bcbio/workflow/template.py' adding 'bcbio/workflow/xprize.py' adding 'bcbio_nextgen-1.1.2.data/scripts/bcbio_fastq_umi_prep.py' adding 'bcbio_nextgen-1.1.2.data/scripts/bcbio_nextgen.py' adding 'bcbio_nextgen-1.1.2.data/scripts/bcbio_prepare_samples.py' adding 'bcbio_nextgen-1.1.2.data/scripts/bcbio_setup_genome.py' adding 'bcbio_nextgen-1.1.2.data/scripts/cwltool2wdl.py' adding 'tests/integration/__init__.py' adding 'tests/integration/test_S3_pipelines.py' adding 'tests/integration/test_SequencingDump.py' adding 'tests/integration/test_automated_analysis.py' adding 'tests/integration/test_pipeline.py' adding 'tests/integration/rnaseq/__init__.py' adding 'tests/integration/rnaseq/test_ericscript.py' adding 'tests/unit/__init__.py' adding 'tests/unit/conftest.py' adding 'tests/unit/data.py' adding 'tests/unit/test_alignprep.py' adding 'tests/unit/distributed/__init__.py' adding 'tests/unit/distributed/test_transaction.py' adding 'tests/unit/ngsalign/__init__.py' adding 'tests/unit/pipeline/__init__.py' adding 'tests/unit/pipeline/test_datadict.py' adding 'tests/unit/pipeline/test_rnaseq.py' adding 'tests/unit/rnaseq/__init__.py' adding 'tests/unit/rnaseq/test_ericscript.py' adding 'tests/unit/upload/__init__.py' adding 'tests/unit/upload/test_upload.py' adding 'bcbio_nextgen-1.1.2.dist-info/LICENSE.txt' adding 'bcbio_nextgen-1.1.2.dist-info/METADATA' adding 'bcbio_nextgen-1.1.2.dist-info/WHEEL' adding 'bcbio_nextgen-1.1.2.dist-info/top_level.txt' adding 'bcbio_nextgen-1.1.2.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Running setup.py bdist_wheel for bcbio-nextgen: finished with status 'done' Stored in directory: /tmp/tmpopc3896q Successfully built bcbio-nextgen Cleaning up... Removing source in /tmp/pip-wheel-rdvjr5gu/bcbio-nextgen Removed build tracker '/tmp/pip-req-tracker-95emwmxi'