biology/cropsr: Add cropsr version 0.0.0.44

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Tue Nov 29 15:45:42 2022 -0700
Changeset:	5abfb8b57cd7ddfed66e7175fc46bd79496fb355

Modified Files:
	Makefile
Added Files:
	cropsr/COMMIT_MSG
	cropsr/DESCR
	cropsr/Makefile
	cropsr/PLIST
	cropsr/distinfo

Log Message:
biology/cropsr: Add cropsr version 0.0.0.44

CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA
Design and Validation

## About CROPSR

CROPSR is a python tool designed for genome-wide gRNA design and
evaluation for CRISPR experiments, with special focus on complex
genomes such as those found in energy-producing crops.  CROPSR is a
product of the DOE Center for Advanced Bioenergy and Bioproducts
Innovation (CABBI).

### Citation

Please cite the following when utilizing CROPSR:

Muller Paul, H., Istanto, D.D., Heldenbrand, J. et al. CROPSR: an
automated platform for complex genome-wide CRISPR gRNA design and
validation. BMC Bioinformatics 23, 74
(2022). https://doi.org/10.1186/s12859-022-04593-2.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5abfb8b57cd7ddfed66e7175fc46bd79496fb355

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

diffstat:
 Makefile          |  1 +
 cropsr/COMMIT_MSG | 22 ++++++++++++++++++++++
 cropsr/DESCR      | 20 ++++++++++++++++++++
 cropsr/Makefile   | 37 +++++++++++++++++++++++++++++++++++++
 cropsr/PLIST      |  8 ++++++++
 cropsr/distinfo   |  5 +++++
 6 files changed, 93 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 397cc27ff2..7c20e64309 100644
--- a/Makefile
+++ b/Makefile
@@ -558,6 +558,7 @@ SUBDIR+=	crispy-doom
 SUBDIR+=	crm114
 SUBDIR+=	cromagrally
 SUBDIR+=	cronolog-devel
+SUBDIR+=	cropsr
 SUBDIR+=	cross-binutils
 SUBDIR+=	crossguid
 SUBDIR+=	crossroads-io
diff --git a/cropsr/COMMIT_MSG b/cropsr/COMMIT_MSG
new file mode 100644
index 0000000000..90e380dc7a
--- /dev/null
+++ b/cropsr/COMMIT_MSG
@@ -0,0 +1,22 @@
+biology/cropsr: Add cropsr version 0.0.0.44
+
+CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA
+Design and Validation
+
+
+## About CROPSR
+
+CROPSR is a python tool designed for genome-wide gRNA design and
+evaluation for CRISPR experiments, with special focus on complex
+genomes such as those found in energy-producing crops.  CROPSR is a
+product of the DOE Center for Advanced Bioenergy and Bioproducts
+Innovation (CABBI).
+
+### Citation
+
+Please cite the following when utilizing CROPSR:
+
+Muller Paul, H., Istanto, D.D., Heldenbrand, J. et al. CROPSR: an
+automated platform for complex genome-wide CRISPR gRNA design and
+validation. BMC Bioinformatics 23, 74
+(2022). https://doi.org/10.1186/s12859-022-04593-2.
diff --git a/cropsr/DESCR b/cropsr/DESCR
new file mode 100644
index 0000000000..6a356faa81
--- /dev/null
+++ b/cropsr/DESCR
@@ -0,0 +1,20 @@
+CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA
+Design and Validation
+
+
+## About CROPSR
+
+CROPSR is a python tool designed for genome-wide gRNA design and
+evaluation for CRISPR experiments, with special focus on complex
+genomes such as those found in energy-producing crops.  CROPSR is a
+product of the DOE Center for Advanced Bioenergy and Bioproducts
+Innovation (CABBI).
+
+### Citation
+
+Please cite the following when utilizing CROPSR:
+
+Muller Paul, H., Istanto, D.D., Heldenbrand, J. et al. CROPSR: an
+automated platform for complex genome-wide CRISPR gRNA design and
+validation. BMC Bioinformatics 23, 74
+(2022). https://doi.org/10.1186/s12859-022-04593-2.
diff --git a/cropsr/Makefile b/cropsr/Makefile
new file mode 100644
index 0000000000..4fee3248a2
--- /dev/null
+++ b/cropsr/Makefile
@@ -0,0 +1,37 @@
+# $NetBSD$
+
+DISTNAME=	CROPSR
+PKGNAME=	cropsr-0.0.0.44
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=H2muller/}
+GITHUB_TAG=	7168556560c4f191fbbd4444fc2be75003abb6db
+GITHUB_TYPE=	tag
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/H2muller/CROPSR
+COMMENT=	Complex genome-wide CRISPR gRNA design and validation
+LICENSE=	apache-2.0
+
+WRKSRC=		${WRKDIR}/${DISTNAME}-${GITHUB_TAG}
+USE_LANGUAGES=	# none
+NO_BUILD=	yes
+
+PYTHON_VERSIONS_INCOMPATIBLE=	27
+
+REPLACE_PYTHON+=	CROPSR.py
+REPLACE_PYTHON+=	cropsr_functions.py
+REPLACE_PYTHON+=	prmrdsgn2.py
+
+INSTALLATION_DIRS+=	bin share/doc/cropsr share/examples/cropsr
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/CROPSR.py ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/cropsr_functions.py ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/prmrdsgn2.py ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/README.md ${DESTDIR}${PREFIX}/share/doc/cropsr
+	${INSTALL_DATA} ${WRKSRC}/sample_data/output.csv ${DESTDIR}${PREFIX}/share/examples/cropsr
+	${INSTALL_DATA} ${WRKSRC}/sample_data/sample_genome.fa ${DESTDIR}${PREFIX}/share/examples/cropsr
+	${INSTALL_DATA} ${WRKSRC}/sample_data/sample_genome.gff ${DESTDIR}${PREFIX}/share/examples/cropsr
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/cropsr/PLIST b/cropsr/PLIST
new file mode 100644
index 0000000000..4ba1a07aeb
--- /dev/null
+++ b/cropsr/PLIST
@@ -0,0 +1,8 @@
+@comment $NetBSD$
+bin/CROPSR.py
+bin/cropsr_functions.py
+bin/prmrdsgn2.py
+share/doc/cropsr/README.md
+share/examples/cropsr/output.csv
+share/examples/cropsr/sample_genome.fa
+share/examples/cropsr/sample_genome.gff
diff --git a/cropsr/distinfo b/cropsr/distinfo
new file mode 100644
index 0000000000..c8345d3057
--- /dev/null
+++ b/cropsr/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (CROPSR-7168556560c4f191fbbd4444fc2be75003abb6db.tar.gz) = 9f92bcdce41edc87c5878c83c17983ce31f5360e84c97c720fa91ff3a722f05a
+SHA512 (CROPSR-7168556560c4f191fbbd4444fc2be75003abb6db.tar.gz) = 08f0d0ae33f8121ef73929e1d96446862a4afb402963d1e0d2c3dedee4cf068db3bf8a8286fa0f12185185911f04ff31c1c2a648797e7cf5b6f4abc43f276df0
+Size (CROPSR-7168556560c4f191fbbd4444fc2be75003abb6db.tar.gz) = 818918 bytes