fastqc: Update to 0.11.9 and clean up

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Jan 19 08:23:44 2021 -0600
Changeset:	a83b7a772da33f1a906fb282fe6564a658be3340

Modified Files:
	fastqc/Makefile
	fastqc/PLIST
	fastqc/distinfo

Log Message:
fastqc: Update to 0.11.9 and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a83b7a772da33f1a906fb282fe6564a658be3340

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

diffstat:
 fastqc/Makefile | 36 ++++++++++++++----------------------
 fastqc/PLIST    | 39 +++++++++++++++++++++++++++++++++++++++
 fastqc/distinfo |  8 ++++----
 3 files changed, 57 insertions(+), 26 deletions(-)

diffs:
diff --git a/fastqc/Makefile b/fastqc/Makefile
index 577d3ac0de..23ce9a5870 100644
--- a/fastqc/Makefile
+++ b/fastqc/Makefile
@@ -5,8 +5,8 @@
 #              Fri Nov  3 16:02:27 CDT 2017               #
 ###########################################################
 
-DISTNAME=	fastqc_v${PORTVERSION}
-PKGNAME=	fastqc-${PORTVERSION}
+DISTNAME=	fastqc_v${PKGVERSION_NOREV}
+PKGNAME=	fastqc-0.11.9
 CATEGORIES=	biology
 MASTER_SITES=	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 EXTRACT_SUFX=	.zip
@@ -14,47 +14,39 @@ EXTRACT_SUFX=	.zip
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 COMMENT=	Quality control tool for high throughput sequence data
-# Check this
 LICENSE=	gnu-gpl-v3
 
 SUBST_CLASSES+=		javapath
-SUBST_STAGE.javapath=	post-patch
+SUBST_STAGE.javapath=	pre-configure
 SUBST_SED.javapath+=	-e 's|$$RealBin$$delimiter|${DATADIR}$$delimiter${JAVAJARDIR}/fastqc$$delimiter|g'
 SUBST_SED.javapath+=	-e 's|$$RealBin/|${JAVAJARDIR}/fastqc/|g'
-SUBST_FILES.javapath+=	${WRKSRC}/fastqc
+SUBST_FILES.javapath+=	fastqc
 
 USE_TOOLS+=	perl:run pax
+USE_JAVA=	yes
+
 REPLACE_PERL=	fastqc
 NO_BUILD=	yes
 
 WRKSRC=		${WRKDIR}/FastQC
 
 # Normal extract is corrupting org/apache/commons/math3/distribution/IntegerDistribution.class due to a bug in archivers/unzip -a
-EXTRACT_OPTS_ZIP=	-qo
+# EXTRACT_OPTS_ZIP=	-qo
 
-PORTVERSION=	0.11.5
 DATADIR=	${PREFIX}/share/fastqc
 DOCSDIR=	${PREFIX}/share/doc/fastqc
-USE_JAVA=	yes
 JAVAJARDIR=	${PREFIX}/share/java/classes
 
 INSTALLATION_DIRS=	bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}/fastqc
 
 do-install:
 	${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}/fastqc
-	${INSTALL_SCRIPT} ${WRKSRC}/fastqc \
-		${DESTDIR}${PREFIX}/bin
-	cd ${WRKSRC} && pax -rw Configuration \
-		${DESTDIR}${DATADIR}
-	cd ${WRKSRC} && pax -rw Templates \
-		${DESTDIR}${DATADIR}
-	cd ${WRKSRC} && pax -rw net \
-		${DESTDIR}${JAVAJARDIR}/fastqc
-	cd ${WRKSRC} && pax -rw org \
-		${DESTDIR}${JAVAJARDIR}/fastqc
-	cd ${WRKSRC} && pax -rw uk \
-		${DESTDIR}${JAVAJARDIR}/fastqc
-	cd ${WRKSRC} && pax -rw 'Help' \
-		${DESTDIR}${DOCSDIR}
+	${INSTALL_SCRIPT} ${WRKSRC}/fastqc ${DESTDIR}${PREFIX}/bin
+	cd ${WRKSRC} && pax -rw Configuration ${DESTDIR}${DATADIR}
+	cd ${WRKSRC} && pax -rw Templates ${DESTDIR}${DATADIR}
+	cd ${WRKSRC} && pax -rw net ${DESTDIR}${JAVAJARDIR}/fastqc
+	cd ${WRKSRC} && pax -rw org ${DESTDIR}${JAVAJARDIR}/fastqc
+	cd ${WRKSRC} && pax -rw uk ${DESTDIR}${JAVAJARDIR}/fastqc
+	cd ${WRKSRC} && pax -rw 'Help' ${DESTDIR}${DOCSDIR}
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/fastqc/PLIST b/fastqc/PLIST
index fe1c64c234..75508fbe9d 100644
--- a/fastqc/PLIST
+++ b/fastqc/PLIST
@@ -1,9 +1,48 @@
 @comment $NetBSD$
 bin/fastqc
+share/doc/fastqc/Help/1 Introduction/.svn/entries
+share/doc/fastqc/Help/1 Introduction/.svn/text-base/1.1 What is FastQC.html.svn-base
 share/doc/fastqc/Help/1 Introduction/1.1 What is FastQC.html
+share/doc/fastqc/Help/2 Basic Operations/.svn/entries
+share/doc/fastqc/Help/2 Basic Operations/.svn/text-base/2.1 Opening a sequence file.html.svn-base
+share/doc/fastqc/Help/2 Basic Operations/.svn/text-base/2.2 Evaluating Results.html.svn-base
+share/doc/fastqc/Help/2 Basic Operations/.svn/text-base/2.3 Saving a Report.html.svn-base
 share/doc/fastqc/Help/2 Basic Operations/2.1 Opening a sequence file.html
 share/doc/fastqc/Help/2 Basic Operations/2.2 Evaluating Results.html
 share/doc/fastqc/Help/2 Basic Operations/2.3 Saving a Report.html
+share/doc/fastqc/Help/3 Analysis Modules/.svn/entries
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/duplication_levels.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/kmer_profiles.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_gc_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_n_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_quality.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_sequence_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_sequence_gc_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_sequence_quality.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_tile_quality.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/sequence_length_distribution.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/1 Basic Statistics.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/10 Adapter Content.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/11 Kmer Content.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/12 Per Tile Sequence Quality.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/2 Per Base Sequence Quality.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/3 Per Sequence Quality Scores.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/4 Per Base Sequence Content.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/5 Per Sequence GC Content.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/6 Per Base N Content.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/7 Sequence Length Distribution.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/8 Duplicate Sequences.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/9 Overrepresented Sequences.html.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/duplication_levels.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/kmer_profiles.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_gc_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_n_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_quality.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_sequence_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_sequence_gc_content.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_sequence_quality.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_tile_quality.png.svn-base
+share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/sequence_length_distribution.png.svn-base
 share/doc/fastqc/Help/3 Analysis Modules/1 Basic Statistics.html
 share/doc/fastqc/Help/3 Analysis Modules/10 Adapter Content.html
 share/doc/fastqc/Help/3 Analysis Modules/11 Kmer Content.html
diff --git a/fastqc/distinfo b/fastqc/distinfo
index 66073d1553..b2d8133dda 100644
--- a/fastqc/distinfo
+++ b/fastqc/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (fastqc_v0.11.5.zip) = 4032cdb7c917c2a97952a91aa9295ab6288f93ad
-RMD160 (fastqc_v0.11.5.zip) = 2bcdbc936d9116f327909fda55cf877421fb02cf
-SHA512 (fastqc_v0.11.5.zip) = 8d12e031294fffa8601d9fbff78fbb3d7d0a7582fd0591d320f8aba856879632912080850aa06c5219dd5690b3396dee0325159ce57f59765eef4b0ce4dc9937
-Size (fastqc_v0.11.5.zip) = 10026429 bytes
+SHA1 (fastqc_v0.11.9.zip) = 077003dcef8933c4b43ac5b6945fdc31b53f746c
+RMD160 (fastqc_v0.11.9.zip) = 9c06aff0044e0f8b4866ae9c731543017e71b9e0
+SHA512 (fastqc_v0.11.9.zip) = f9ed1546d08e941abcca8ff507d2cf2d455831fcb3d36def7d9881f4f23c4d7874b62d28c5f9901149e1b5bc7ca5fe746c5a522785b7fe72bc9e96330b568bed
+Size (fastqc_v0.11.9.zip) = 10249221 bytes