py-multiqc: Aggregate bioinformatics analysis reports

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jul 19 15:51:24 2023 -0500
Changeset:	0c2b73af64df3df00d09ad175778776017e76772

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

Log Message:
py-multiqc: Aggregate bioinformatics analysis 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 see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=0c2b73af64df3df00d09ad175778776017e76772

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

diffstat:
 Makefile                                    |  1 +
 py-multiqc/DESCR                            |  3 ++
 py-multiqc/Makefile                         | 51 +++++++++++++++++++++++++++++
 py-multiqc/PLIST                            |  1 +
 py-multiqc/distinfo                         |  5 +++
 py-multiqc/patches/patch-multiqc_multiqc.py | 19 +++++++++++
 6 files changed, 80 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index fab52c797e..91d9e9213b 100644
--- a/Makefile
+++ b/Makefile
@@ -4132,6 +4132,7 @@ SUBDIR+=	py-msumastro
 SUBDIR+=	py-multichain_mcmc
 SUBDIR+=	py-multimethods
 SUBDIR+=	py-multiprocess
+SUBDIR+=	py-multiqc
 SUBDIR+=	py-multitasking
 SUBDIR+=	py-multivar-horner
 SUBDIR+=	py-munch
diff --git a/py-multiqc/DESCR b/py-multiqc/DESCR
new file mode 100644
index 0000000000..e4eb84c16e
--- /dev/null
+++ b/py-multiqc/DESCR
@@ -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.
diff --git a/py-multiqc/Makefile b/py-multiqc/Makefile
new file mode 100644
index 0000000000..a9ed5bac74
--- /dev/null
+++ b/py-multiqc/Makefile
@@ -0,0 +1,51 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed Jul 19 15:14:18 CDT 2023               #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# Need to package these deps
+# RUN_DEPENDS=	${PYNUMPY} \
+#		${PYPKGPREFIX}-rich-click>0:devel/py-rich-click@${PY_FLAVOR}
+#		${PYPKGPREFIX}-lzstring>0:archivers/py-lzstring@${PY_FLAVOR}
+#		${PYPKGPREFIX}-spectra>=0.0.10:graphics/py-spectra@${PY_FLAVOR}
+
+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}-future-[0-9]*:../../devel/py-future
+DEPENDS+=	${PYPKGPREFIX}-coloredlogs>=3.5:../../wip/py-coloredlogs
+DEPENDS+=	${PYPKGPREFIX}-matplotlib-[0-9]*:../../graphics/py-matplotlib
+DEPENDS+=	${PYPKGPREFIX}-markdown-[0-9]*:../../textproc/py-markdown
+DEPENDS+=	${PYPKGPREFIX}-markdown-[0-9]*:../../textproc/py-markdown
+DEPENDS+=	${PYPKGPREFIX}-markdown-[0-9]*:../../textproc/py-markdown
+DEPENDS+=	${PYPKGPREFIX}-yaml>=3.13:../../textproc/py-yaml
+DEPENDS+=	${PYPKGPREFIX}-requests>=2.2.1:../../devel/py-requests
+DEPENDS+=	${PYPKGPREFIX}-simplejson>=3.6.5:../../converters/py-simplejson
+DEPENDS+=	${PYPKGPREFIX}-jinja2>=2.3<3:../../textproc/py-jinja2
+DEPENDS+=	${PYPKGPREFIX}-kiwisolver>=1.0.1:../../math/py-kiwisolver
+DEPENDS+=	${PYPKGPREFIX}-colormath>0:../../wip/py-colormath
+
+post-patch:
+	@${RM} ${WRKSRC}/multiqc/utils/config.py.orig
+
+# Verify that we shouldn't use distutils.mk or extensions.mk instead.
+.include "../../lang/python/egg.mk"
+# Convert any _DEPENDS above that have a buildlink3.mk
+# .include "../..///buildlink3.mk"
+# Based on USES=python.  Check this.
+.include "../../lang/python/application.mk"
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-multiqc/PLIST b/py-multiqc/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/py-multiqc/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/py-multiqc/distinfo b/py-multiqc/distinfo
new file mode 100644
index 0000000000..4aa1775c35
--- /dev/null
+++ b/py-multiqc/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (multiqc-1.14.tar.gz) = c242a4114ee7e84cb98c646d997d29445ad0886c6345c88a5189be4ebf986d20
+SHA512 (multiqc-1.14.tar.gz) = 4dca7bcc94ae1906812046984c2aee0d48ec58987483b27a29c473798f4ed06ded33d0b7e1a46c71642392c6c39f7cc1cee6d97cfdabd80c42eb519be7c86e9f
+Size (multiqc-1.14.tar.gz) = 1054868 bytes
diff --git a/py-multiqc/patches/patch-multiqc_multiqc.py b/py-multiqc/patches/patch-multiqc_multiqc.py
new file mode 100644
index 0000000000..eaf391b216
--- /dev/null
+++ b/py-multiqc/patches/patch-multiqc_multiqc.py
@@ -0,0 +1,19 @@
+$NetBSD$
+
+--- 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