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xmatchview: import xmatchview-1.2.5 as wip/xmatchview

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Sat Jun 19 21:28:56 2021 -0600
Changeset:	af1e53365272113104f66c251c6c8725a76a5a29

Modified Files:
	Makefile
Added Files:
	xmatchview/DESCR
	xmatchview/Makefile
	xmatchview/PLIST
	xmatchview/distinfo
	xmatchview/patches/patch-test_runXMV.sh
	xmatchview/patches/patch-xmatchview-conifer.py
	xmatchview/patches/patch-xmatchview-hive.py

Log Message:
xmatchview: import xmatchview-1.2.5 as wip/xmatchview

xmatchview, xmatchview-conifer and xmatchview-hive are imaging tools
for visualizing DNA/RNA sequence synteny. It allows users to align 2
(or 3) sequences in FASTA format using cross_match, minimap2 or any
aligners with .paf output capabilities, and displays the alignments in
a variety of image formats (png, tiff). xmatchview-hive outputs
xml-scalable vector graphics (svg).

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=af1e53365272113104f66c251c6c8725a76a5a29

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

diffstat:
 Makefile                                       |  1 +
 xmatchview/DESCR                               |  6 ++++
 xmatchview/Makefile                            | 43 ++++++++++++++++++++++++++
 xmatchview/PLIST                               |  7 +++++
 xmatchview/distinfo                            |  9 ++++++
 xmatchview/patches/patch-test_runXMV.sh        | 13 ++++++++
 xmatchview/patches/patch-xmatchview-conifer.py | 15 +++++++++
 xmatchview/patches/patch-xmatchview-hive.py    | 15 +++++++++
 8 files changed, 109 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 14889be687..d3574d4c2f 100644
--- a/Makefile
+++ b/Makefile
@@ -5844,6 +5844,7 @@ SUBDIR+=	xinvaders3d
 SUBDIR+=	xlossage-git
 SUBDIR+=	xmail
 SUBDIR+=	xmakemol
+SUBDIR+=	xmatchview
 SUBDIR+=	xmds
 SUBDIR+=	xmim
 SUBDIR+=	xml-light
diff --git a/xmatchview/DESCR b/xmatchview/DESCR
new file mode 100644
index 0000000000..a19f9c710b
--- /dev/null
+++ b/xmatchview/DESCR
@@ -0,0 +1,6 @@
+xmatchview, xmatchview-conifer and xmatchview-hive are imaging tools
+for visualizing DNA/RNA sequence synteny. It allows users to align 2
+(or 3) sequences in FASTA format using cross_match, minimap2 or any
+aligners with .paf output capabilities, and displays the alignments in
+a variety of image formats (png, tiff). xmatchview-hive outputs
+xml-scalable vector graphics (svg).
diff --git a/xmatchview/Makefile b/xmatchview/Makefile
new file mode 100644
index 0000000000..494f22d10d
--- /dev/null
+++ b/xmatchview/Makefile
@@ -0,0 +1,43 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	xmatchview
+GITHUB_TAG=	refs/tags/v1.2.5
+DISTNAME=	v1.2.5
+PKGNAME=	${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=bcgsc/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/bcgsc/xmatchview/
+COMMENT=	Genome alignment visualization
+LICENSE=	gnu-gpl-v3
+
+WRKSRC=		${WRKDIR}/xmatchview-1.2.5
+USE_LANGUAGES=	# none
+NO_BUILD=	yes
+
+DEPENDS+=	${PYPKGPREFIX}-Pillow>=8.2.0:../../wip/py-pillow
+
+REPLACE_PYTHON+=	xmatchview-conifer.py
+REPLACE_PYTHON+=	xmatchview-hive.py
+REPLACE_PYTHON+=	xmatchview.py
+
+INSTALLATION_DIRS+=	bin share/doc/xmatchview
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/xmatchview-conifer.py ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/xmatchview-hive.py ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/xmatchview.py ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/README.md ${DESTDIR}${PREFIX}/share/doc/xmatchview
+	${INSTALL_DATA} ${WRKSRC}/paper/paper.md ${DESTDIR}${PREFIX}/share/doc/xmatchview
+	${INSTALL_DATA} ${WRKSRC}/paper/paper.pdf ${DESTDIR}${PREFIX}/share/doc/xmatchview
+
+do-test:
+	cd ${WRKSRC}/test \
+	&& ./runXMV.sh FTL1_pa.fa_vs_FTL1_ss.fa.rep FTL1_pa.fa FTL1_ss.fa 200 10 2 FTL1_pa.gff FTL1_ss.gff
+	cd ${WRKSRC}/test-hive \
+	&& ../xmatchview-hive.py -q 2019-nCoV.txt -r SARS-CoV.txt -s MERS-CoV.txt -x 2019-nCoV.fa_vs_SARS-CoV.fa.rep -y 2019-nCoV.fa_vs_MERS-CoV.fa.rep -z MERS-CoV.fa_vs_SARS-CoV.fa.rep -e SARScds.gff -i 0 -b 1 -c 30 -a 0.75
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/xmatchview/PLIST b/xmatchview/PLIST
new file mode 100644
index 0000000000..9fa46bdcbf
--- /dev/null
+++ b/xmatchview/PLIST
@@ -0,0 +1,7 @@
+@comment $NetBSD$
+bin/xmatchview-conifer.py
+bin/xmatchview-hive.py
+bin/xmatchview.py
+share/doc/xmatchview/README.md
+share/doc/xmatchview/paper.md
+share/doc/xmatchview/paper.pdf
diff --git a/xmatchview/distinfo b/xmatchview/distinfo
new file mode 100644
index 0000000000..46d0c8ec13
--- /dev/null
+++ b/xmatchview/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+SHA1 (xmatchview/v1.2.5.tar.gz) = 5d01e604a498229055e11df1a921b983401a22d5
+RMD160 (xmatchview/v1.2.5.tar.gz) = 6ebfaac69670e3b574fc55b32686e7625a0e7076
+SHA512 (xmatchview/v1.2.5.tar.gz) = 9eb7b793ba07a29583a1a9efd82d0f93af8933a639359ef695c4327ff7b4c7a9c8b3db10cb1e3c58648c6af5d1077c59672ecc6ef641f4194195ed64247d7a1e
+Size (xmatchview/v1.2.5.tar.gz) = 15709995 bytes
+SHA1 (patch-test_runXMV.sh) = d1545c1b520b8399d18cab878186c2847ec9977f
+SHA1 (patch-xmatchview-conifer.py) = 6aba8a24d03a82af09cbc41f641cbc3921067468
+SHA1 (patch-xmatchview-hive.py) = 41491423ea3247b120c5eaf5cabadc48ef3ff706
diff --git a/xmatchview/patches/patch-test_runXMV.sh b/xmatchview/patches/patch-test_runXMV.sh
new file mode 100644
index 0000000000..3e02b17f1d
--- /dev/null
+++ b/xmatchview/patches/patch-test_runXMV.sh
@@ -0,0 +1,13 @@
+$NetBSD$
+
+Run script directly so python version is correct.
+
+--- test/runXMV.sh.orig	2020-10-27 18:34:34.000000000 +0000
++++ test/runXMV.sh
+@@ -9,5 +9,5 @@ if [ $# -ne 8 ]; then
+ fi
+ 
+ # source PATH-TO-SOURCE (IF NEEDED)
+-python3 ../xmatchview.py -x $1 -s $3 -q $2 -a $4 -m $5 -b 10 -r 1 -c $6 -f png -y $7 -e $8 -p ../../tarballs/fonts
++../xmatchview.py -x $1 -s $3 -q $2 -a $4 -m $5 -b 10 -r 1 -c $6 -f png -y $7 -e $8 -p ../../tarballs/fonts
+ 
diff --git a/xmatchview/patches/patch-xmatchview-conifer.py b/xmatchview/patches/patch-xmatchview-conifer.py
new file mode 100644
index 0000000000..d78e92228b
--- /dev/null
+++ b/xmatchview/patches/patch-xmatchview-conifer.py
@@ -0,0 +1,15 @@
+$NetBSD$
+
+Do not return an error after successful completion.
+
+See https://github.com/bcgsc/xmatchview/issues/12.
+
+--- xmatchview-conifer.py.orig	2021-06-20 00:25:31.000000000 +0000
++++ xmatchview-conifer.py
+@@ -1104,6 +1104,5 @@ def main():
+ #Main Call
+ 
+ main()
+-sys.exit(1)
+ 
+ 
diff --git a/xmatchview/patches/patch-xmatchview-hive.py b/xmatchview/patches/patch-xmatchview-hive.py
new file mode 100644
index 0000000000..702999d6f8
--- /dev/null
+++ b/xmatchview/patches/patch-xmatchview-hive.py
@@ -0,0 +1,15 @@
+$NetBSD$
+
+Do not return an error after successful completion.
+
+See https://github.com/bcgsc/xmatchview/issues/12.
+
+--- xmatchview-hive.py.orig	2021-06-20 00:25:31.000000000 +0000
++++ xmatchview-hive.py
+@@ -1047,6 +1047,5 @@ def main():
+ #Main Call
+ 
+ main()
+-sys.exit(1)
+ 
+
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