Created temporary directory: /tmp/pip-ephem-wheel-cache-xi1y07si Created temporary directory: /tmp/pip-req-tracker-4epn0p7h Created requirements tracker '/tmp/pip-req-tracker-4epn0p7h' Created temporary directory: /tmp/pip-wheel-jk6w7sau Collecting biobakery-workflows==0.13.4 1 location(s) to search for versions of biobakery-workflows: * https://pypi.org/simple/biobakery-workflows/ Getting page https://pypi.org/simple/biobakery-workflows/ Analyzing links from page https://pypi.org/simple/biobakery-workflows/ Found link https://files.pythonhosted.org/packages/1c/b8/2d49305112ddce416e9f37d6bbd9cdd50eeda669d91954e9b4188b00aa9c/biobakery_workflows-0.3.0.tar.gz#sha256=40fb7921f8bf721b0179672ea42220e43627e2fbf2cc9ec71225f1b405406e05 (from https://pypi.org/simple/biobakery-workflows/), version: 0.3.0 Found link https://files.pythonhosted.org/packages/70/7c/64769accee73cfba802fd536ca6b19990bfd444dc429038a0b0e970d4707/biobakery_workflows-0.3.1.tar.gz#sha256=8ffadeb2c57595a33a01a3f1d341191eff0dcc1acd33280496fe220ceb02ebe9 (from https://pypi.org/simple/biobakery-workflows/), version: 0.3.1 Found link https://files.pythonhosted.org/packages/10/51/511c7456972a3e51fb98416e153eaaf2f2e091683763a9030bcfd9278dee/biobakery_workflows-0.9.0.tar.gz#sha256=80496a31a267472bdfc434ad52f4a38d896fece5817f87cf37f9010882d75298 (from https://pypi.org/simple/biobakery-workflows/), version: 0.9.0 Found link https://files.pythonhosted.org/packages/26/56/14a401341149cc14532ab03e8e327c21518b3e03c07ab4f8b9469abc4d11/biobakery_workflows-0.12.1.tar.gz#sha256=d5f6f0a73e5e30d0fb5ef198296ac8ad7d63813e098b6963ee27b6f606d12042 (from https://pypi.org/simple/biobakery-workflows/), version: 0.12.1 Found link https://files.pythonhosted.org/packages/10/5f/a627ee61e221c02dc272c5d77c2208be7f47e274f0241cc4a6052b5c17eb/biobakery_workflows-0.13.0.tar.gz#sha256=6cbf6df4e2cf77f6c8ddb21ac03137747ce1561775464eab8dc74b8b91c4b729 (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.0 Found link https://files.pythonhosted.org/packages/51/63/a9f0055e5c798017111b959383b92a79d77716a8aae668353f46985f48da/biobakery_workflows-0.13.1.tar.gz#sha256=8d57bffdd3d67bef378537046f0a4c54bb855d0ae8dab8c97d027b680e9050ab (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.1 Found link https://files.pythonhosted.org/packages/4b/5f/e8a487a22758156034d8a9ecd9846f10383e610780cd8b5d90ecfb32faf9/biobakery_workflows-0.13.2.tar.gz#sha256=93b5ecf1f5395149a9021516a0cc3e2a7cb2c9c4c5c1ebefc5f5822bcfdbf6b4 (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.2 Found link https://files.pythonhosted.org/packages/cc/87/d006df9363f78ade3e5c766c61113ad96d18036e2cca432c6f174fa87340/biobakery_workflows-0.13.3.tar.gz#sha256=211e600d24e0ef0c654265b914b2181b92a635d2a4bbab4773c890ab5aa06574 (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.3 Found link https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz#sha256=7f5d6637ca83ec1df74277110fc65bc8bc75aed5ff10c923b6f5fb15cb7fec3f (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.4 Using version 0.13.4 (newest of versions: 0.13.4) Created temporary directory: /tmp/pip-unpack-husf7wsu Downloading https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz (44.6MB) Downloading from URL https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz#sha256=7f5d6637ca83ec1df74277110fc65bc8bc75aed5ff10c923b6f5fb15cb7fec3f (from https://pypi.org/simple/biobakery-workflows/) Added biobakery-workflows==0.13.4 from https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz#sha256=7f5d6637ca83ec1df74277110fc65bc8bc75aed5ff10c923b6f5fb15cb7fec3f to build tracker '/tmp/pip-req-tracker-4epn0p7h' Running setup.py (path:/tmp/pip-wheel-jk6w7sau/biobakery-workflows/setup.py) egg_info for package biobakery-workflows Running command python setup.py egg_info Downloading counter file to track biobakery_workflows downloads since the global PyPI download stats are currently turned off. Downloading http://bitbucket.org/biobakery/biobakery_workflows/downloads/counter.txt running egg_info creating pip-egg-info/biobakery_workflows.egg-info writing pip-egg-info/biobakery_workflows.egg-info/PKG-INFO writing dependency_links to pip-egg-info/biobakery_workflows.egg-info/dependency_links.txt writing top-level names to pip-egg-info/biobakery_workflows.egg-info/top_level.txt writing requirements to pip-egg-info/biobakery_workflows.egg-info/requires.txt writing entry points to pip-egg-info/biobakery_workflows.egg-info/entry_points.txt writing manifest file 'pip-egg-info/biobakery_workflows.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/biobakery_workflows.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pip-egg-info/biobakery_workflows.egg-info/SOURCES.txt' Source in /tmp/pip-wheel-jk6w7sau/biobakery-workflows has version 0.13.4, which satisfies requirement biobakery-workflows==0.13.4 from https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz#sha256=7f5d6637ca83ec1df74277110fc65bc8bc75aed5ff10c923b6f5fb15cb7fec3f Removed biobakery-workflows==0.13.4 from https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz#sha256=7f5d6637ca83ec1df74277110fc65bc8bc75aed5ff10c923b6f5fb15cb7fec3f from build tracker '/tmp/pip-req-tracker-4epn0p7h' Building wheels for collected packages: biobakery-workflows Created temporary directory: /tmp/pip-wheel-2zgnfn3m Running setup.py bdist_wheel for biobakery-workflows: started Destination directory: /tmp/pip-wheel-2zgnfn3m Running command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-wheel-jk6w7sau/biobakery-workflows/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-2zgnfn3m running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/biobakery_workflows copying biobakery_workflows/__init__.py -> build/lib/biobakery_workflows copying biobakery_workflows/visualizations.py -> build/lib/biobakery_workflows copying biobakery_workflows/config.py -> build/lib/biobakery_workflows copying biobakery_workflows/biobakery_workflows.py -> build/lib/biobakery_workflows copying biobakery_workflows/utilities.py -> build/lib/biobakery_workflows copying biobakery_workflows/files.py -> build/lib/biobakery_workflows copying biobakery_workflows/biobakery_workflows_databases.py -> build/lib/biobakery_workflows creating build/lib/tests copying tests/__init__.py -> build/lib/tests copying tests/test_utilities.py -> build/lib/tests creating build/lib/biobakery_workflows/data copying biobakery_workflows/data/__init__.py -> build/lib/biobakery_workflows/data creating build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/__init__.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/header.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/taxonomy.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/16S.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/functional_dna_rna.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/functional_dna.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/quality_control_paired_dna_rna.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/quality_control_paired_dna.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/workflow_info.template.py -> build/lib/biobakery_workflows/document_templates copying biobakery_workflows/document_templates/quality_control_single_dna.template.py -> build/lib/biobakery_workflows/document_templates creating build/lib/biobakery_workflows/tasks copying biobakery_workflows/tasks/__init__.py -> build/lib/biobakery_workflows/tasks copying biobakery_workflows/tasks/sixteen_s.py -> build/lib/biobakery_workflows/tasks copying biobakery_workflows/tasks/shotgun.py -> build/lib/biobakery_workflows/tasks copying biobakery_workflows/tasks/dadatwo.py -> build/lib/biobakery_workflows/tasks copying biobakery_workflows/tasks/general.py -> build/lib/biobakery_workflows/tasks creating build/lib/biobakery_workflows/workflows copying biobakery_workflows/workflows/16s_vis.py -> build/lib/biobakery_workflows/workflows copying biobakery_workflows/workflows/wmgx_wmtx.py -> build/lib/biobakery_workflows/workflows copying biobakery_workflows/workflows/wmgx_wmtx_vis.py -> build/lib/biobakery_workflows/workflows copying biobakery_workflows/workflows/16s.py -> build/lib/biobakery_workflows/workflows copying biobakery_workflows/workflows/wmgx.py -> build/lib/biobakery_workflows/workflows copying biobakery_workflows/workflows/wmgx_vis.py -> build/lib/biobakery_workflows/workflows copying biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/lib/biobakery_workflows/data creating build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/const_seq_table.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/phylogeny.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/filter_and_trim.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/dada2_version.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/learn_error_rates.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/assign_taxonomy.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/merge_paired_ends.R -> build/lib/biobakery_workflows/Rscripts copying biobakery_workflows/Rscripts/identify_primers.R -> build/lib/biobakery_workflows/Rscripts running build_scripts creating build/scripts-3.4 copying and adjusting biobakery_workflows/workflows/16s_vis.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/workflows/wmgx_wmtx.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/workflows/wmgx_wmtx_vis.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/workflows/16s.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/workflows/wmgx.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/workflows/wmgx_vis.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/create_otu_tables_from_alignments.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/merge_and_rename_fastq.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/extract_orphan_reads.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/create_fasta_per_taxonomy_from_alignments.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/reverse_compliment_barcodes.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/remove_if_exists.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/count_features.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/merge_fastq.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/generate_dual_barcode.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/demultiplex_split_index.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/rename_fastq_files.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/create_subsampled_demos.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/get_counts_from_humann2_logs.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/trim_taxonomy.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/check_fastq_format.py -> build/scripts-3.4 copying and adjusting biobakery_workflows/scripts/rna_dna_norm.py -> build/scripts-3.4 changing mode of build/scripts-3.4/16s_vis.py from 644 to 755 changing mode of build/scripts-3.4/wmgx_wmtx.py from 644 to 755 changing mode of build/scripts-3.4/wmgx_wmtx_vis.py from 644 to 755 changing mode of build/scripts-3.4/16s.py from 644 to 755 changing mode of build/scripts-3.4/wmgx.py from 644 to 755 changing mode of build/scripts-3.4/wmgx_vis.py from 644 to 755 changing mode of build/scripts-3.4/create_otu_tables_from_alignments.py from 644 to 755 changing mode of build/scripts-3.4/merge_and_rename_fastq.py from 644 to 755 changing mode of build/scripts-3.4/extract_orphan_reads.py from 644 to 755 changing mode of build/scripts-3.4/create_fasta_per_taxonomy_from_alignments.py from 644 to 755 changing mode of build/scripts-3.4/reverse_compliment_barcodes.py from 644 to 755 changing mode of build/scripts-3.4/remove_if_exists.py from 644 to 755 changing mode of build/scripts-3.4/count_features.py from 644 to 755 changing mode of build/scripts-3.4/merge_fastq.py from 644 to 755 changing mode of build/scripts-3.4/generate_dual_barcode.py from 644 to 755 changing mode of build/scripts-3.4/demultiplex_split_index.py from 644 to 755 changing mode of build/scripts-3.4/rename_fastq_files.py from 644 to 755 changing mode of build/scripts-3.4/create_subsampled_demos.py from 644 to 755 changing mode of build/scripts-3.4/get_counts_from_humann2_logs.py from 644 to 755 changing mode of build/scripts-3.4/trim_taxonomy.py from 644 to 755 changing mode of build/scripts-3.4/check_fastq_format.py from 644 to 755 changing mode of build/scripts-3.4/rna_dna_norm.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/biobakery_workflows creating build/bdist.linux-armv7l/wheel/biobakery_workflows/data copying build/lib/biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data copying build/lib/biobakery_workflows/data/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data creating build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/workflows/16s_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/workflows/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/workflows/wmgx_wmtx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/workflows/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/workflows/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/workflows/wmgx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows copying build/lib/biobakery_workflows/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows creating build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/header.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/taxonomy.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/16S.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/functional_dna_rna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/functional_dna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/quality_control_paired_dna_rna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/quality_control_paired_dna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/workflow_info.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/document_templates/quality_control_single_dna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates copying build/lib/biobakery_workflows/visualizations.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows copying build/lib/biobakery_workflows/config.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows copying build/lib/biobakery_workflows/biobakery_workflows.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows copying build/lib/biobakery_workflows/utilities.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows copying build/lib/biobakery_workflows/files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows creating build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks copying build/lib/biobakery_workflows/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks copying build/lib/biobakery_workflows/tasks/sixteen_s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks copying build/lib/biobakery_workflows/tasks/shotgun.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks copying build/lib/biobakery_workflows/tasks/dadatwo.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks copying build/lib/biobakery_workflows/tasks/general.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks creating build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/const_seq_table.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/phylogeny.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/filter_and_trim.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/dada2_version.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/learn_error_rates.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/assign_taxonomy.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/merge_paired_ends.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/Rscripts/identify_primers.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts copying build/lib/biobakery_workflows/biobakery_workflows_databases.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows creating build/bdist.linux-armv7l/wheel/tests copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests copying build/lib/tests/test_utilities.py -> build/bdist.linux-armv7l/wheel/tests running install_data creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input copying examples/tutorial/input/HD42R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input/ copying examples/tutorial/input/LV16R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input/ copying examples/tutorial/input/HD32R1_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input/ copying examples/tutorial/input/HD48R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input/ copying examples/tutorial/input/LD96R2_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input/ copying examples/tutorial/input/LV20R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/input/ creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/ creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/ copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/ copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/ copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/ copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/ copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/ running install_egg_info running egg_info writing dependency_links to biobakery_workflows.egg-info/dependency_links.txt writing top-level names to biobakery_workflows.egg-info/top_level.txt writing requirements to biobakery_workflows.egg-info/requires.txt writing biobakery_workflows.egg-info/PKG-INFO writing entry points to biobakery_workflows.egg-info/entry_points.txt reading manifest file 'biobakery_workflows.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'biobakery_workflows.egg-info/SOURCES.txt' Copying biobakery_workflows.egg-info to build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4-py3.4.egg-info running install_scripts creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/16s_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/create_otu_tables_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/merge_and_rename_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/extract_orphan_reads.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/create_fasta_per_taxonomy_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/reverse_compliment_barcodes.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/remove_if_exists.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/count_features.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/merge_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/wmgx_wmtx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/generate_dual_barcode.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/demultiplex_split_index.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/rename_fastq_files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/create_subsampled_demos.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/get_counts_from_humann2_logs.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/wmgx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/trim_taxonomy.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/check_fastq_format.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts copying build/scripts-3.4/rna_dna_norm.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/16s_vis.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/wmgx_wmtx.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/create_otu_tables_from_alignments.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/merge_and_rename_fastq.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/extract_orphan_reads.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/create_fasta_per_taxonomy_from_alignments.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/reverse_compliment_barcodes.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/remove_if_exists.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/count_features.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/merge_fastq.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/wmgx_wmtx_vis.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/generate_dual_barcode.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/demultiplex_split_index.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/rename_fastq_files.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/16s.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/create_subsampled_demos.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/wmgx.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/get_counts_from_humann2_logs.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/wmgx_vis.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/trim_taxonomy.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/check_fastq_format.py to 755 changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.data/scripts/rna_dna_norm.py to 755 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") creating build/bdist.linux-armv7l/wheel/biobakery_workflows-0.13.4.dist-info/WHEEL creating '/tmp/pip-wheel-2zgnfn3m/biobakery_workflows-0.13.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it adding 'biobakery_workflows/__init__.py' adding 'biobakery_workflows/biobakery_workflows.py' adding 'biobakery_workflows/biobakery_workflows_databases.py' adding 'biobakery_workflows/config.py' adding 'biobakery_workflows/files.py' adding 'biobakery_workflows/utilities.py' adding 'biobakery_workflows/visualizations.py' adding 'biobakery_workflows/Rscripts/assign_taxonomy.R' adding 'biobakery_workflows/Rscripts/const_seq_table.R' adding 'biobakery_workflows/Rscripts/dada2_version.R' adding 'biobakery_workflows/Rscripts/filter_and_trim.R' adding 'biobakery_workflows/Rscripts/identify_primers.R' adding 'biobakery_workflows/Rscripts/learn_error_rates.R' adding 'biobakery_workflows/Rscripts/merge_paired_ends.R' adding 'biobakery_workflows/Rscripts/phylogeny.R' adding 'biobakery_workflows/data/__init__.py' adding 'biobakery_workflows/data/strainphlan_species_gcf.tsv' adding 'biobakery_workflows/document_templates/16S.template.py' adding 'biobakery_workflows/document_templates/__init__.py' adding 'biobakery_workflows/document_templates/functional_dna.template.py' adding 'biobakery_workflows/document_templates/functional_dna_rna.template.py' adding 'biobakery_workflows/document_templates/header.template.py' adding 'biobakery_workflows/document_templates/quality_control_paired_dna.template.py' adding 'biobakery_workflows/document_templates/quality_control_paired_dna_rna.template.py' adding 'biobakery_workflows/document_templates/quality_control_single_dna.template.py' adding 'biobakery_workflows/document_templates/taxonomy.template.py' adding 'biobakery_workflows/document_templates/workflow_info.template.py' adding 'biobakery_workflows/tasks/__init__.py' adding 'biobakery_workflows/tasks/dadatwo.py' adding 'biobakery_workflows/tasks/general.py' adding 'biobakery_workflows/tasks/shotgun.py' adding 'biobakery_workflows/tasks/sixteen_s.py' adding 'biobakery_workflows/workflows/16s.py' adding 'biobakery_workflows/workflows/16s_vis.py' adding 'biobakery_workflows/workflows/wmgx.py' adding 'biobakery_workflows/workflows/wmgx_vis.py' adding 'biobakery_workflows/workflows/wmgx_wmtx.py' adding 'biobakery_workflows/workflows/wmgx_wmtx_vis.py' adding 'biobakery_workflows-0.13.4.data/data/tutorial/input/HD32R1_subsample.fastq.gz' adding 'biobakery_workflows-0.13.4.data/data/tutorial/input/HD42R4_subsample.fastq.gz' adding 'biobakery_workflows-0.13.4.data/data/tutorial/input/HD48R4_subsample.fastq.gz' adding 'biobakery_workflows-0.13.4.data/data/tutorial/input/LD96R2_subsample.fastq.gz' adding 'biobakery_workflows-0.13.4.data/data/tutorial/input/LV16R4_subsample.fastq.gz' adding 'biobakery_workflows-0.13.4.data/data/tutorial/input/LV20R4_subsample.fastq.gz' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.1.bt2' adding 'biobakery_workflows-0.13.4.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.2.bt2' adding 'biobakery_workflows-0.13.4.data/scripts/16s.py' adding 'biobakery_workflows-0.13.4.data/scripts/16s_vis.py' adding 'biobakery_workflows-0.13.4.data/scripts/check_fastq_format.py' adding 'biobakery_workflows-0.13.4.data/scripts/count_features.py' adding 'biobakery_workflows-0.13.4.data/scripts/create_fasta_per_taxonomy_from_alignments.py' adding 'biobakery_workflows-0.13.4.data/scripts/create_otu_tables_from_alignments.py' adding 'biobakery_workflows-0.13.4.data/scripts/create_subsampled_demos.py' adding 'biobakery_workflows-0.13.4.data/scripts/demultiplex_split_index.py' adding 'biobakery_workflows-0.13.4.data/scripts/extract_orphan_reads.py' adding 'biobakery_workflows-0.13.4.data/scripts/generate_dual_barcode.py' adding 'biobakery_workflows-0.13.4.data/scripts/get_counts_from_humann2_logs.py' adding 'biobakery_workflows-0.13.4.data/scripts/merge_and_rename_fastq.py' adding 'biobakery_workflows-0.13.4.data/scripts/merge_fastq.py' adding 'biobakery_workflows-0.13.4.data/scripts/remove_if_exists.py' adding 'biobakery_workflows-0.13.4.data/scripts/rename_fastq_files.py' adding 'biobakery_workflows-0.13.4.data/scripts/reverse_compliment_barcodes.py' adding 'biobakery_workflows-0.13.4.data/scripts/rna_dna_norm.py' adding 'biobakery_workflows-0.13.4.data/scripts/trim_taxonomy.py' adding 'biobakery_workflows-0.13.4.data/scripts/wmgx.py' adding 'biobakery_workflows-0.13.4.data/scripts/wmgx_vis.py' adding 'biobakery_workflows-0.13.4.data/scripts/wmgx_wmtx.py' adding 'biobakery_workflows-0.13.4.data/scripts/wmgx_wmtx_vis.py' adding 'tests/__init__.py' adding 'tests/test_utilities.py' adding 'biobakery_workflows-0.13.4.dist-info/LICENSE' adding 'biobakery_workflows-0.13.4.dist-info/METADATA' adding 'biobakery_workflows-0.13.4.dist-info/WHEEL' adding 'biobakery_workflows-0.13.4.dist-info/entry_points.txt' adding 'biobakery_workflows-0.13.4.dist-info/top_level.txt' adding 'biobakery_workflows-0.13.4.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Running setup.py bdist_wheel for biobakery-workflows: finished with status 'done' Stored in directory: /tmp/tmpofcrzfyx Successfully built biobakery-workflows Cleaning up... Removing source in /tmp/pip-wheel-jk6w7sau/biobakery-workflows Removed build tracker '/tmp/pip-req-tracker-4epn0p7h'