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CVS commit: pkgsrc/biology/py-multiqc

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Jul 22 13:18:53 UTC 2023

Added Files:
        pkgsrc/biology/py-multiqc: DESCR Makefile PLIST distinfo
        pkgsrc/biology/py-multiqc/patches: patch-multiqc_multiqc.py

Log Message:
biology/py-multiqc: Aggregate bioinformatics reports

MultiQC searches a given directory for analysis logs and compiles an HTML
report. It's a general use tool, perfect for summarising the output from
numerous bioinformatics tools.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/py-multiqc/DESCR \
    pkgsrc/biology/py-multiqc/Makefile pkgsrc/biology/py-multiqc/PLIST \
    pkgsrc/biology/py-multiqc/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/py-multiqc/patches/patch-multiqc_multiqc.py

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.


Added files:

Index: pkgsrc/biology/py-multiqc/DESCR
diff -u /dev/null pkgsrc/biology/py-multiqc/DESCR:1.1
--- /dev/null   Sat Jul 22 13:18:53 2023
+++ pkgsrc/biology/py-multiqc/DESCR     Sat Jul 22 13:18:52 2023
@@ -0,0 +1,3 @@
+MultiQC searches a given directory for analysis logs and compiles an HTML
+report. It's a general use tool, perfect for summarising the output from
+numerous bioinformatics tools.
Index: pkgsrc/biology/py-multiqc/Makefile
diff -u /dev/null pkgsrc/biology/py-multiqc/Makefile:1.1
--- /dev/null   Sat Jul 22 13:18:53 2023
+++ pkgsrc/biology/py-multiqc/Makefile  Sat Jul 22 13:18:52 2023
@@ -0,0 +1,33 @@
+# $NetBSD: Makefile,v 1.1 2023/07/22 13:18:52 bacon Exp $
+
+DISTNAME=      multiqc-1.14
+PKGNAME=       ${PYPKGPREFIX}-multiqc-1.14
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_PYPI:=m/multiqc/}
+
+OWNER=         bacon%NetBSD.org@localhost
+HOMEPAGE=      https://pypi.python.org/pypi/multiqc
+COMMENT=       Aggregate bioinformatics analysis reports across samples and tools
+LICENSE=       gnu-gpl-v3
+
+DEPENDS+=      ${PYPKGPREFIX}-matplotlib>=2.1.1:../../graphics/py-matplotlib
+DEPENDS+=      ${PYPKGPREFIX}-networkx>=2.5.1:../../math/py-networkx
+DEPENDS+=      ${PYPKGPREFIX}-click-[0-9]*:../../devel/py-click
+DEPENDS+=      ${PYPKGPREFIX}-coloredlogs-[0-9]*:../../devel/py-coloredlogs
+DEPENDS+=      ${PYPKGPREFIX}-future>0.14.0:../../devel/py-future
+DEPENDS+=      ${PYPKGPREFIX}-jinja2>=3.0.0:../../textproc/py-jinja2
+DEPENDS+=      ${PYPKGPREFIX}-markdown-[0-9]*:../../textproc/py-markdown
+DEPENDS+=      ${PYPKGPREFIX}-yaml>=4:../../textproc/py-yaml
+DEPENDS+=      ${PYPKGPREFIX}-requests-[0-9]*:../../devel/py-requests
+DEPENDS+=      ${PYPKGPREFIX}-rich>=10:../../comms/py-rich
+DEPENDS+=      ${PYPKGPREFIX}-rich-click-[0-9]*:../../devel/py-rich-click
+DEPENDS+=      ${PYPKGPREFIX}-simplejson-[0-9]*:../../converters/py-simplejson
+DEPENDS+=      ${PYPKGPREFIX}-spectra>=0.0.10:../../graphics/py-spectra
+DEPENDS+=      ${PYPKGPREFIX}-lzstring>0:../../archivers/py-lzstring
+
+post-patch:
+       ${RM} ${WRKSRC}/multiqc/multiqc.py.orig
+
+.include "../../lang/python/egg.mk"
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/py-multiqc/PLIST
diff -u /dev/null pkgsrc/biology/py-multiqc/PLIST:1.1
--- /dev/null   Sat Jul 22 13:18:53 2023
+++ pkgsrc/biology/py-multiqc/PLIST     Sat Jul 22 13:18:52 2023
@@ -0,0 +1,1247 @@
+@comment $NetBSD: PLIST,v 1.1 2023/07/22 13:18:52 bacon Exp $
+bin/multiqc
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/multiqc/__init__.py
+${PYSITELIB}/multiqc/__init__.pyc
+${PYSITELIB}/multiqc/__init__.pyo
+${PYSITELIB}/multiqc/__main__.py
+${PYSITELIB}/multiqc/__main__.pyc
+${PYSITELIB}/multiqc/__main__.pyo
+${PYSITELIB}/multiqc/modules/__init__.py
+${PYSITELIB}/multiqc/modules/__init__.pyc
+${PYSITELIB}/multiqc/modules/__init__.pyo
+${PYSITELIB}/multiqc/modules/adapterRemoval/__init__.py
+${PYSITELIB}/multiqc/modules/adapterRemoval/__init__.pyc
+${PYSITELIB}/multiqc/modules/adapterRemoval/__init__.pyo
+${PYSITELIB}/multiqc/modules/adapterRemoval/adapterRemoval.py
+${PYSITELIB}/multiqc/modules/adapterRemoval/adapterRemoval.pyc
+${PYSITELIB}/multiqc/modules/adapterRemoval/adapterRemoval.pyo
+${PYSITELIB}/multiqc/modules/afterqc/__init__.py
+${PYSITELIB}/multiqc/modules/afterqc/__init__.pyc
+${PYSITELIB}/multiqc/modules/afterqc/__init__.pyo
+${PYSITELIB}/multiqc/modules/afterqc/afterqc.py
+${PYSITELIB}/multiqc/modules/afterqc/afterqc.pyc
+${PYSITELIB}/multiqc/modules/afterqc/afterqc.pyo
+${PYSITELIB}/multiqc/modules/anglerfish/__init__.py
+${PYSITELIB}/multiqc/modules/anglerfish/__init__.pyc
+${PYSITELIB}/multiqc/modules/anglerfish/__init__.pyo
+${PYSITELIB}/multiqc/modules/anglerfish/anglerfish.py
+${PYSITELIB}/multiqc/modules/anglerfish/anglerfish.pyc
+${PYSITELIB}/multiqc/modules/anglerfish/anglerfish.pyo
+${PYSITELIB}/multiqc/modules/bamtools/__init__.py
+${PYSITELIB}/multiqc/modules/bamtools/__init__.pyc
+${PYSITELIB}/multiqc/modules/bamtools/__init__.pyo
+${PYSITELIB}/multiqc/modules/bamtools/bamtools.py
+${PYSITELIB}/multiqc/modules/bamtools/bamtools.pyc
+${PYSITELIB}/multiqc/modules/bamtools/bamtools.pyo
+${PYSITELIB}/multiqc/modules/bamtools/stats.py
+${PYSITELIB}/multiqc/modules/bamtools/stats.pyc
+${PYSITELIB}/multiqc/modules/bamtools/stats.pyo
+${PYSITELIB}/multiqc/modules/base_module.py
+${PYSITELIB}/multiqc/modules/base_module.pyc
+${PYSITELIB}/multiqc/modules/base_module.pyo
+${PYSITELIB}/multiqc/modules/bbduk/__init__.py
+${PYSITELIB}/multiqc/modules/bbduk/__init__.pyc
+${PYSITELIB}/multiqc/modules/bbduk/__init__.pyo
+${PYSITELIB}/multiqc/modules/bbduk/bbduk.py
+${PYSITELIB}/multiqc/modules/bbduk/bbduk.pyc
+${PYSITELIB}/multiqc/modules/bbduk/bbduk.pyo
+${PYSITELIB}/multiqc/modules/bbmap/__init__.py
+${PYSITELIB}/multiqc/modules/bbmap/__init__.pyc
+${PYSITELIB}/multiqc/modules/bbmap/__init__.pyo
+${PYSITELIB}/multiqc/modules/bbmap/bbmap.py
+${PYSITELIB}/multiqc/modules/bbmap/bbmap.pyc
+${PYSITELIB}/multiqc/modules/bbmap/bbmap.pyo
+${PYSITELIB}/multiqc/modules/bbmap/bbmap_filetypes.py
+${PYSITELIB}/multiqc/modules/bbmap/bbmap_filetypes.pyc
+${PYSITELIB}/multiqc/modules/bbmap/bbmap_filetypes.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_aqhist.py
+${PYSITELIB}/multiqc/modules/bbmap/plot_aqhist.pyc
+${PYSITELIB}/multiqc/modules/bbmap/plot_aqhist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_basic_hist.py
+${PYSITELIB}/multiqc/modules/bbmap/plot_basic_hist.pyc
+${PYSITELIB}/multiqc/modules/bbmap/plot_basic_hist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_bhist.py
+${PYSITELIB}/multiqc/modules/bbmap/plot_bhist.pyc
+${PYSITELIB}/multiqc/modules/bbmap/plot_bhist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_bqhist.py
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+${PYSITELIB}/multiqc/modules/bbmap/plot_covhist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_idhist.py
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+${PYSITELIB}/multiqc/modules/bbmap/plot_idhist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_ihist.py
+${PYSITELIB}/multiqc/modules/bbmap/plot_ihist.pyc
+${PYSITELIB}/multiqc/modules/bbmap/plot_ihist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_indelhist.py
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+${PYSITELIB}/multiqc/modules/bbmap/plot_mhist.py
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+${PYSITELIB}/multiqc/modules/bbmap/plot_mhist.pyo
+${PYSITELIB}/multiqc/modules/bbmap/plot_qahist.py
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+${PYSITELIB}/multiqc/modules/bbmap/plot_qahist.pyo
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+${PYSITELIB}/multiqc/modules/bcftools/__init__.pyc
+${PYSITELIB}/multiqc/modules/bcftools/__init__.pyo
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+${PYSITELIB}/multiqc/modules/bcftools/stats.pyo
+${PYSITELIB}/multiqc/modules/bcl2fastq/__init__.py
+${PYSITELIB}/multiqc/modules/bcl2fastq/__init__.pyc
+${PYSITELIB}/multiqc/modules/bcl2fastq/__init__.pyo
+${PYSITELIB}/multiqc/modules/bcl2fastq/bcl2fastq.py
+${PYSITELIB}/multiqc/modules/bcl2fastq/bcl2fastq.pyc
+${PYSITELIB}/multiqc/modules/bcl2fastq/bcl2fastq.pyo
+${PYSITELIB}/multiqc/modules/bclconvert/__init__.py
+${PYSITELIB}/multiqc/modules/bclconvert/__init__.pyc
+${PYSITELIB}/multiqc/modules/bclconvert/__init__.pyo
+${PYSITELIB}/multiqc/modules/bclconvert/bclconvert.py
+${PYSITELIB}/multiqc/modules/bclconvert/bclconvert.pyc
+${PYSITELIB}/multiqc/modules/bclconvert/bclconvert.pyo
+${PYSITELIB}/multiqc/modules/biobambam2/__init__.py
+${PYSITELIB}/multiqc/modules/biobambam2/__init__.pyc
+${PYSITELIB}/multiqc/modules/biobambam2/__init__.pyo
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+${PYSITELIB}/multiqc/modules/biobloomtools/__init__.py
+${PYSITELIB}/multiqc/modules/biobloomtools/__init__.pyc
+${PYSITELIB}/multiqc/modules/biobloomtools/__init__.pyo
+${PYSITELIB}/multiqc/modules/biobloomtools/biobloomtools.py
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+${PYSITELIB}/multiqc/modules/biscuit/__init__.pyc
+${PYSITELIB}/multiqc/modules/biscuit/__init__.pyo
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+${PYSITELIB}/multiqc/modules/bowtie2/__init__.pyo
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+${PYSITELIB}/multiqc/modules/cellranger/_utils.py
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+${PYSITELIB}/multiqc/modules/disambiguate/disambiguate.py
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+${PYSITELIB}/multiqc/modules/disambiguate/disambiguate.pyo
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+${PYSITELIB}/multiqc/modules/sentieon/__init__.pyc
+${PYSITELIB}/multiqc/modules/sentieon/__init__.pyo
+${PYSITELIB}/multiqc/modules/sentieon/sentieon.py
+${PYSITELIB}/multiqc/modules/sentieon/sentieon.pyc
+${PYSITELIB}/multiqc/modules/sentieon/sentieon.pyo
+${PYSITELIB}/multiqc/modules/seqyclean/__init__.py
+${PYSITELIB}/multiqc/modules/seqyclean/__init__.pyc
+${PYSITELIB}/multiqc/modules/seqyclean/__init__.pyo
+${PYSITELIB}/multiqc/modules/seqyclean/seqyclean.py
+${PYSITELIB}/multiqc/modules/seqyclean/seqyclean.pyc
+${PYSITELIB}/multiqc/modules/seqyclean/seqyclean.pyo
+${PYSITELIB}/multiqc/modules/sexdeterrmine/__init__.py
+${PYSITELIB}/multiqc/modules/sexdeterrmine/__init__.pyc
+${PYSITELIB}/multiqc/modules/sexdeterrmine/__init__.pyo
+${PYSITELIB}/multiqc/modules/sexdeterrmine/sexdeterrmine.py
+${PYSITELIB}/multiqc/modules/sexdeterrmine/sexdeterrmine.pyc
+${PYSITELIB}/multiqc/modules/sexdeterrmine/sexdeterrmine.pyo
+${PYSITELIB}/multiqc/modules/sickle/__init__.py
+${PYSITELIB}/multiqc/modules/sickle/__init__.pyc
+${PYSITELIB}/multiqc/modules/sickle/__init__.pyo
+${PYSITELIB}/multiqc/modules/sickle/sickle.py
+${PYSITELIB}/multiqc/modules/sickle/sickle.pyc
+${PYSITELIB}/multiqc/modules/sickle/sickle.pyo
+${PYSITELIB}/multiqc/modules/skewer/__init__.py
+${PYSITELIB}/multiqc/modules/skewer/__init__.pyc
+${PYSITELIB}/multiqc/modules/skewer/__init__.pyo
+${PYSITELIB}/multiqc/modules/skewer/skewer.py
+${PYSITELIB}/multiqc/modules/skewer/skewer.pyc
+${PYSITELIB}/multiqc/modules/skewer/skewer.pyo
+${PYSITELIB}/multiqc/modules/slamdunk/__init__.py
+${PYSITELIB}/multiqc/modules/slamdunk/__init__.pyc
+${PYSITELIB}/multiqc/modules/slamdunk/__init__.pyo
+${PYSITELIB}/multiqc/modules/slamdunk/slamdunk.py
+${PYSITELIB}/multiqc/modules/slamdunk/slamdunk.pyc
+${PYSITELIB}/multiqc/modules/slamdunk/slamdunk.pyo
+${PYSITELIB}/multiqc/modules/snippy/__init__.py
+${PYSITELIB}/multiqc/modules/snippy/__init__.pyc
+${PYSITELIB}/multiqc/modules/snippy/__init__.pyo
+${PYSITELIB}/multiqc/modules/snippy/snippy.py
+${PYSITELIB}/multiqc/modules/snippy/snippy.pyc
+${PYSITELIB}/multiqc/modules/snippy/snippy.pyo
+${PYSITELIB}/multiqc/modules/snpeff/__init__.py
+${PYSITELIB}/multiqc/modules/snpeff/__init__.pyc
+${PYSITELIB}/multiqc/modules/snpeff/__init__.pyo
+${PYSITELIB}/multiqc/modules/snpeff/snpeff.py
+${PYSITELIB}/multiqc/modules/snpeff/snpeff.pyc
+${PYSITELIB}/multiqc/modules/snpeff/snpeff.pyo
+${PYSITELIB}/multiqc/modules/snpsplit/__init__.py
+${PYSITELIB}/multiqc/modules/snpsplit/__init__.pyc
+${PYSITELIB}/multiqc/modules/snpsplit/__init__.pyo
+${PYSITELIB}/multiqc/modules/snpsplit/snpsplit.py
+${PYSITELIB}/multiqc/modules/snpsplit/snpsplit.pyc
+${PYSITELIB}/multiqc/modules/snpsplit/snpsplit.pyo
+${PYSITELIB}/multiqc/modules/somalier/__init__.py
+${PYSITELIB}/multiqc/modules/somalier/__init__.pyc
+${PYSITELIB}/multiqc/modules/somalier/__init__.pyo
+${PYSITELIB}/multiqc/modules/somalier/somalier.py
+${PYSITELIB}/multiqc/modules/somalier/somalier.pyc
+${PYSITELIB}/multiqc/modules/somalier/somalier.pyo
+${PYSITELIB}/multiqc/modules/sortmerna/__init__.py
+${PYSITELIB}/multiqc/modules/sortmerna/__init__.pyc
+${PYSITELIB}/multiqc/modules/sortmerna/__init__.pyo
+${PYSITELIB}/multiqc/modules/sortmerna/sortmerna.py
+${PYSITELIB}/multiqc/modules/sortmerna/sortmerna.pyc
+${PYSITELIB}/multiqc/modules/sortmerna/sortmerna.pyo
+${PYSITELIB}/multiqc/modules/stacks/__init__.py
+${PYSITELIB}/multiqc/modules/stacks/__init__.pyc
+${PYSITELIB}/multiqc/modules/stacks/__init__.pyo
+${PYSITELIB}/multiqc/modules/stacks/stacks.py
+${PYSITELIB}/multiqc/modules/stacks/stacks.pyc
+${PYSITELIB}/multiqc/modules/stacks/stacks.pyo
+${PYSITELIB}/multiqc/modules/star/__init__.py
+${PYSITELIB}/multiqc/modules/star/__init__.pyc
+${PYSITELIB}/multiqc/modules/star/__init__.pyo
+${PYSITELIB}/multiqc/modules/star/star.py
+${PYSITELIB}/multiqc/modules/star/star.pyc
+${PYSITELIB}/multiqc/modules/star/star.pyo
+${PYSITELIB}/multiqc/modules/supernova/__init__.py
+${PYSITELIB}/multiqc/modules/supernova/__init__.pyc
+${PYSITELIB}/multiqc/modules/supernova/__init__.pyo
+${PYSITELIB}/multiqc/modules/supernova/supernova.py
+${PYSITELIB}/multiqc/modules/supernova/supernova.pyc
+${PYSITELIB}/multiqc/modules/supernova/supernova.pyo
+${PYSITELIB}/multiqc/modules/theta2/__init__.py
+${PYSITELIB}/multiqc/modules/theta2/__init__.pyc
+${PYSITELIB}/multiqc/modules/theta2/__init__.pyo
+${PYSITELIB}/multiqc/modules/theta2/theta2.py
+${PYSITELIB}/multiqc/modules/theta2/theta2.pyc
+${PYSITELIB}/multiqc/modules/theta2/theta2.pyo
+${PYSITELIB}/multiqc/modules/tophat/__init__.py
+${PYSITELIB}/multiqc/modules/tophat/__init__.pyc
+${PYSITELIB}/multiqc/modules/tophat/__init__.pyo
+${PYSITELIB}/multiqc/modules/tophat/tophat.py
+${PYSITELIB}/multiqc/modules/tophat/tophat.pyc
+${PYSITELIB}/multiqc/modules/tophat/tophat.pyo
+${PYSITELIB}/multiqc/modules/trimmomatic/__init__.py
+${PYSITELIB}/multiqc/modules/trimmomatic/__init__.pyc
+${PYSITELIB}/multiqc/modules/trimmomatic/__init__.pyo
+${PYSITELIB}/multiqc/modules/trimmomatic/trimmomatic.py
+${PYSITELIB}/multiqc/modules/trimmomatic/trimmomatic.pyc
+${PYSITELIB}/multiqc/modules/trimmomatic/trimmomatic.pyo
+${PYSITELIB}/multiqc/modules/umitools/__init__.py
+${PYSITELIB}/multiqc/modules/umitools/__init__.pyc
+${PYSITELIB}/multiqc/modules/umitools/__init__.pyo
+${PYSITELIB}/multiqc/modules/umitools/umitools.py
+${PYSITELIB}/multiqc/modules/umitools/umitools.pyc
+${PYSITELIB}/multiqc/modules/umitools/umitools.pyo
+${PYSITELIB}/multiqc/modules/varscan2/__init__.py
+${PYSITELIB}/multiqc/modules/varscan2/__init__.pyc
+${PYSITELIB}/multiqc/modules/varscan2/__init__.pyo
+${PYSITELIB}/multiqc/modules/varscan2/varscan2.py
+${PYSITELIB}/multiqc/modules/varscan2/varscan2.pyc
+${PYSITELIB}/multiqc/modules/varscan2/varscan2.pyo
+${PYSITELIB}/multiqc/modules/vcftools/__init__.py
+${PYSITELIB}/multiqc/modules/vcftools/__init__.pyc
+${PYSITELIB}/multiqc/modules/vcftools/__init__.pyo
+${PYSITELIB}/multiqc/modules/vcftools/relatedness2.py
+${PYSITELIB}/multiqc/modules/vcftools/relatedness2.pyc
+${PYSITELIB}/multiqc/modules/vcftools/relatedness2.pyo
+${PYSITELIB}/multiqc/modules/vcftools/tstv_by_count.py
+${PYSITELIB}/multiqc/modules/vcftools/tstv_by_count.pyc
+${PYSITELIB}/multiqc/modules/vcftools/tstv_by_count.pyo
+${PYSITELIB}/multiqc/modules/vcftools/tstv_by_qual.py
+${PYSITELIB}/multiqc/modules/vcftools/tstv_by_qual.pyc
+${PYSITELIB}/multiqc/modules/vcftools/tstv_by_qual.pyo
+${PYSITELIB}/multiqc/modules/vcftools/tstv_summary.py
+${PYSITELIB}/multiqc/modules/vcftools/tstv_summary.pyc
+${PYSITELIB}/multiqc/modules/vcftools/tstv_summary.pyo
+${PYSITELIB}/multiqc/modules/vcftools/vcftools.py
+${PYSITELIB}/multiqc/modules/vcftools/vcftools.pyc
+${PYSITELIB}/multiqc/modules/vcftools/vcftools.pyo
+${PYSITELIB}/multiqc/modules/vep/__init__.py
+${PYSITELIB}/multiqc/modules/vep/__init__.pyc
+${PYSITELIB}/multiqc/modules/vep/__init__.pyo
+${PYSITELIB}/multiqc/modules/vep/vep.py
+${PYSITELIB}/multiqc/modules/vep/vep.pyc
+${PYSITELIB}/multiqc/modules/vep/vep.pyo
+${PYSITELIB}/multiqc/modules/verifybamid/__init__.py
+${PYSITELIB}/multiqc/modules/verifybamid/__init__.pyc
+${PYSITELIB}/multiqc/modules/verifybamid/__init__.pyo
+${PYSITELIB}/multiqc/modules/verifybamid/verifybamid.py
+${PYSITELIB}/multiqc/modules/verifybamid/verifybamid.pyc
+${PYSITELIB}/multiqc/modules/verifybamid/verifybamid.pyo
+${PYSITELIB}/multiqc/modules/whatshap/__init__.py
+${PYSITELIB}/multiqc/modules/whatshap/__init__.pyc
+${PYSITELIB}/multiqc/modules/whatshap/__init__.pyo
+${PYSITELIB}/multiqc/modules/whatshap/whatshap.py
+${PYSITELIB}/multiqc/modules/whatshap/whatshap.pyc
+${PYSITELIB}/multiqc/modules/whatshap/whatshap.pyo
+${PYSITELIB}/multiqc/multiqc.py
+${PYSITELIB}/multiqc/multiqc.pyc
+${PYSITELIB}/multiqc/multiqc.pyo
+${PYSITELIB}/multiqc/plots/__init__.py
+${PYSITELIB}/multiqc/plots/__init__.pyc
+${PYSITELIB}/multiqc/plots/__init__.pyo
+${PYSITELIB}/multiqc/plots/bargraph.py
+${PYSITELIB}/multiqc/plots/bargraph.pyc
+${PYSITELIB}/multiqc/plots/bargraph.pyo
+${PYSITELIB}/multiqc/plots/beeswarm.py
+${PYSITELIB}/multiqc/plots/beeswarm.pyc
+${PYSITELIB}/multiqc/plots/beeswarm.pyo
+${PYSITELIB}/multiqc/plots/boxplot.py
+${PYSITELIB}/multiqc/plots/boxplot.pyc
+${PYSITELIB}/multiqc/plots/boxplot.pyo
+${PYSITELIB}/multiqc/plots/heatmap.py
+${PYSITELIB}/multiqc/plots/heatmap.pyc
+${PYSITELIB}/multiqc/plots/heatmap.pyo
+${PYSITELIB}/multiqc/plots/linegraph.py
+${PYSITELIB}/multiqc/plots/linegraph.pyc
+${PYSITELIB}/multiqc/plots/linegraph.pyo
+${PYSITELIB}/multiqc/plots/scatter.py
+${PYSITELIB}/multiqc/plots/scatter.pyc
+${PYSITELIB}/multiqc/plots/scatter.pyo
+${PYSITELIB}/multiqc/plots/table.py
+${PYSITELIB}/multiqc/plots/table.pyc
+${PYSITELIB}/multiqc/plots/table.pyo
+${PYSITELIB}/multiqc/plots/table_object.py
+${PYSITELIB}/multiqc/plots/table_object.pyc
+${PYSITELIB}/multiqc/plots/table_object.pyo
+${PYSITELIB}/multiqc/templates/__init__.py
+${PYSITELIB}/multiqc/templates/__init__.pyc
+${PYSITELIB}/multiqc/templates/__init__.pyo
+${PYSITELIB}/multiqc/templates/default/__init__.py
+${PYSITELIB}/multiqc/templates/default/__init__.pyc
+${PYSITELIB}/multiqc/templates/default/__init__.pyo
+${PYSITELIB}/multiqc/templates/default/assets/css/bootstrap.min.css
+${PYSITELIB}/multiqc/templates/default/assets/css/default_multiqc.css
+${PYSITELIB}/multiqc/templates/default/assets/css/jquery.toast.css
+${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.eot
+${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.svg
+${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
+${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff
+${PYSITELIB}/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff2
+${PYSITELIB}/multiqc/templates/default/assets/img/MultiQC_logo.png
+${PYSITELIB}/multiqc/templates/default/assets/img/Seqera-Labs.png
+${PYSITELIB}/multiqc/templates/default/assets/img/favicon-16x16.png
+${PYSITELIB}/multiqc/templates/default/assets/img/favicon-32x32.png
+${PYSITELIB}/multiqc/templates/default/assets/img/favicon-96x96.png
+${PYSITELIB}/multiqc/templates/default/assets/js/multiqc.js
+${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_mpl.js
+${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_plotting.js
+${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_tables.js
+${PYSITELIB}/multiqc/templates/default/assets/js/multiqc_toolbox.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/FileSaver.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/bootstrap.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/clipboard.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.export-csv.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.exporting.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.heatmap.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/highcharts.offline-exporting.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery-ui.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/jquery.toast.min.js
+${PYSITELIB}/multiqc/templates/default/assets/js/packages/lz-string.min.js
+${PYSITELIB}/multiqc/templates/default/base.html
+${PYSITELIB}/multiqc/templates/default/content.html
+${PYSITELIB}/multiqc/templates/default/foot.html
+${PYSITELIB}/multiqc/templates/default/footer.html
+${PYSITELIB}/multiqc/templates/default/general_stats.html
+${PYSITELIB}/multiqc/templates/default/head.html
+${PYSITELIB}/multiqc/templates/default/header.html
+${PYSITELIB}/multiqc/templates/default/includes.html
+${PYSITELIB}/multiqc/templates/default/nav.html
+${PYSITELIB}/multiqc/templates/default/toolbox.html
+${PYSITELIB}/multiqc/templates/default_dev/__init__.py
+${PYSITELIB}/multiqc/templates/default_dev/__init__.pyc
+${PYSITELIB}/multiqc/templates/default_dev/__init__.pyo
+${PYSITELIB}/multiqc/templates/default_dev/includes.html
+${PYSITELIB}/multiqc/templates/gathered/__init__.py
+${PYSITELIB}/multiqc/templates/gathered/__init__.pyc
+${PYSITELIB}/multiqc/templates/gathered/__init__.pyo
+${PYSITELIB}/multiqc/templates/gathered/content.html
+${PYSITELIB}/multiqc/templates/gathered/nav.html
+${PYSITELIB}/multiqc/templates/geo/__init__.py
+${PYSITELIB}/multiqc/templates/geo/__init__.pyc
+${PYSITELIB}/multiqc/templates/geo/__init__.pyo
+${PYSITELIB}/multiqc/templates/geo/assets/css/bootstrap.min.css
+${PYSITELIB}/multiqc/templates/geo/assets/img/emailme.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/flames.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/glyphicons-halflings-white.png
+${PYSITELIB}/multiqc/templates/geo/assets/img/glyphicons-halflings.png
+${PYSITELIB}/multiqc/templates/geo/assets/img/hot.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/mchammer.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/microfab.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/new.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/new2.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/progress.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/rainbow.gif
+${PYSITELIB}/multiqc/templates/geo/assets/img/stars.gif
+${PYSITELIB}/multiqc/templates/geo/includes.html
+${PYSITELIB}/multiqc/templates/sections/__init__.py
+${PYSITELIB}/multiqc/templates/sections/__init__.pyc
+${PYSITELIB}/multiqc/templates/sections/__init__.pyo
+${PYSITELIB}/multiqc/templates/sections/content.html
+${PYSITELIB}/multiqc/templates/simple/__init__.py
+${PYSITELIB}/multiqc/templates/simple/__init__.pyc
+${PYSITELIB}/multiqc/templates/simple/__init__.pyo
+${PYSITELIB}/multiqc/templates/simple/foot.html
+${PYSITELIB}/multiqc/templates/simple/header.html
+${PYSITELIB}/multiqc/templates/simple/includes.html
+${PYSITELIB}/multiqc/templates/simple/nav.html
+${PYSITELIB}/multiqc/templates/simple/toolbox.html
+${PYSITELIB}/multiqc/utils/__init__.py
+${PYSITELIB}/multiqc/utils/__init__.pyc
+${PYSITELIB}/multiqc/utils/__init__.pyo
+${PYSITELIB}/multiqc/utils/config.py
+${PYSITELIB}/multiqc/utils/config.pyc
+${PYSITELIB}/multiqc/utils/config.pyo
+${PYSITELIB}/multiqc/utils/config_defaults.yaml
+${PYSITELIB}/multiqc/utils/lint_helpers.py
+${PYSITELIB}/multiqc/utils/lint_helpers.pyc
+${PYSITELIB}/multiqc/utils/lint_helpers.pyo
+${PYSITELIB}/multiqc/utils/log.py
+${PYSITELIB}/multiqc/utils/log.pyc
+${PYSITELIB}/multiqc/utils/log.pyo
+${PYSITELIB}/multiqc/utils/megaqc.py
+${PYSITELIB}/multiqc/utils/megaqc.pyc
+${PYSITELIB}/multiqc/utils/megaqc.pyo
+${PYSITELIB}/multiqc/utils/mqc_colour.py
+${PYSITELIB}/multiqc/utils/mqc_colour.pyc
+${PYSITELIB}/multiqc/utils/mqc_colour.pyo
+${PYSITELIB}/multiqc/utils/plugin_hooks.py
+${PYSITELIB}/multiqc/utils/plugin_hooks.pyc
+${PYSITELIB}/multiqc/utils/plugin_hooks.pyo
+${PYSITELIB}/multiqc/utils/profile_runtime.py
+${PYSITELIB}/multiqc/utils/profile_runtime.pyc
+${PYSITELIB}/multiqc/utils/profile_runtime.pyo
+${PYSITELIB}/multiqc/utils/report.py
+${PYSITELIB}/multiqc/utils/report.pyc
+${PYSITELIB}/multiqc/utils/report.pyo
+${PYSITELIB}/multiqc/utils/search_patterns.yaml
+${PYSITELIB}/multiqc/utils/util_functions.py
+${PYSITELIB}/multiqc/utils/util_functions.pyc
+${PYSITELIB}/multiqc/utils/util_functions.pyo
Index: pkgsrc/biology/py-multiqc/distinfo
diff -u /dev/null pkgsrc/biology/py-multiqc/distinfo:1.1
--- /dev/null   Sat Jul 22 13:18:53 2023
+++ pkgsrc/biology/py-multiqc/distinfo  Sat Jul 22 13:18:52 2023
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2023/07/22 13:18:52 bacon Exp $
+
+BLAKE2s (multiqc-1.14.tar.gz) = c242a4114ee7e84cb98c646d997d29445ad0886c6345c88a5189be4ebf986d20
+SHA512 (multiqc-1.14.tar.gz) = 4dca7bcc94ae1906812046984c2aee0d48ec58987483b27a29c473798f4ed06ded33d0b7e1a46c71642392c6c39f7cc1cee6d97cfdabd80c42eb519be7c86e9f
+Size (multiqc-1.14.tar.gz) = 1054868 bytes
+SHA1 (patch-multiqc_multiqc.py) = 666b3c1a7af2a05582d38540fbfdc32a264120ff

Index: pkgsrc/biology/py-multiqc/patches/patch-multiqc_multiqc.py
diff -u /dev/null pkgsrc/biology/py-multiqc/patches/patch-multiqc_multiqc.py:1.1
--- /dev/null   Sat Jul 22 13:18:53 2023
+++ pkgsrc/biology/py-multiqc/patches/patch-multiqc_multiqc.py  Sat Jul 22 13:18:53 2023
@@ -0,0 +1,21 @@
+$NetBSD: patch-multiqc_multiqc.py,v 1.1 2023/07/22 13:18:53 bacon Exp $
+
+# Ensure proper terminal output
+
+--- multiqc/multiqc.py.orig    2023-05-11 13:19:10 UTC
++++ multiqc/multiqc.py
+@@ -24,7 +24,13 @@ from urllib.request import urlopen
+ 
+ import jinja2
+ import rich
+-import rich_click as click
++if 'LC_ALL' in os.environ and 'LANG' in os.environ:
++    import rich_click as click
++else:
++    print('multiqc: LC_ALL and LANG must be set to a UTF-8 character set')
++    print('in your environment in order for the click module to function.')
++    print('E.g. export LC_ALL=en_US.UTF-8 or setenv LC_ALL en_US.UTF-8')
++    sys.exit()
+ from rich.syntax import Syntax
+ 
+ from .plots import table
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