fastqc: Manual extract to work around corruption issue

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 17 12:57:00 2017 -0600
Changeset:	b82ce9e0f60af3bd222ff1a8119707317505d227

Modified Files:
	fastqc/Makefile

Log Message:
fastqc: Manual extract to work around corruption issue

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=b82ce9e0f60af3bd222ff1a8119707317505d227

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

diffstat:
 fastqc/Makefile | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diffs:
diff --git a/fastqc/Makefile b/fastqc/Makefile
index e7662f00e1..1afddc7fae 100644
--- a/fastqc/Makefile
+++ b/fastqc/Makefile
@@ -8,7 +8,7 @@
 DISTNAME=	fastqc_v${PORTVERSION}
 PKGNAME=	fastqc-${PORTVERSION}
 CATEGORIES=	biology
-MASTER_SITES=	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+MASTER_SITES=	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 EXTRACT_SUFX=	.zip
 
 MAINTAINER=	bacon4000%gmail.com@localhost
@@ -37,6 +37,10 @@ JAVAJARDIR=	${PREFIX}/share/java/classes
 
 INSTALLATION_DIRS=	bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}/fastqc
 
+# Normal extract is corrupting org/apache/commons/math3/distribution/IntegerDistribution.class
+do-extract:
+	cd ${WRKDIR} && unzip ${DISTDIR}/${DISTFILES}
+
 do-install:
 	${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}/fastqc
 	${INSTALL_SCRIPT} ${WRKSRC}/fastqc \