bowtie2: Add doc and examples to INSTALLATION_DIRS

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jan 20 19:06:01 2021 -0600
Changeset:	a195cdd954e33049e98d47ab00bcda10acd915af

Modified Files:
	bowtie2/Makefile
	bowtie2/PLIST
Removed Files:
	bowtie2/files/bowtie2-manual

Log Message:
bowtie2: Add doc and examples to INSTALLATION_DIRS

Oddly only necessary on Darwin

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a195cdd954e33049e98d47ab00bcda10acd915af

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

diffstat:
 bowtie2/Makefile             | 13 ++++---------
 bowtie2/PLIST                |  1 -
 bowtie2/files/bowtie2-manual |  4 ----
 3 files changed, 4 insertions(+), 14 deletions(-)

diffs:
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
index 31c523f504..d62ed8ca28 100644
--- a/bowtie2/Makefile
+++ b/bowtie2/Makefile
@@ -1,9 +1,4 @@
 # $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Wed Mar  2 08:06:07 CST 2016               #
-###########################################################
 
 DISTNAME=	bowtie2-2.4.2
 CATEGORIES=	biology
@@ -16,11 +11,11 @@ COMMENT=	Ultrafast, memory-efficient short read aligner
 LICENSE=	gnu-gpl-v3
 
 USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake perl:run pax
+USE_TOOLS+=	gmake pax:build perl:run
 REPLACE_PERL=	scripts/*.pl bowtie2
 REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
 
-# TBB is a little challenging, so use pthreads until onetbb is committed
+# Use onetbb on supported platforms when a package is available
 MAKE_FLAGS+=	NO_TBB=1
 
 DATADIR=	${PREFIX}/share/bowtie2
@@ -28,14 +23,14 @@ DOCSDIR=	${PREFIX}/share/doc/bowtie2
 EXAMPLESDIR=	${PREFIX}/share/examples/bowtie2
 
 INSTALLATION_DIRS=	share/bowtie2/scripts
+INSTALLATION_DIRS+=	share/doc/bowtie2
+INSTALLATION_DIRS+=	share/examples/bowtie2
 
 post-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/bowtie2*-s ${WRKSRC}/bowtie2*-l \
 		${DESTDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/*.sh ${WRKSRC}/scripts/*.pl \
 		${DESTDIR}${DATADIR}/scripts
-	${INSTALL_SCRIPT} ${FILESDIR}/bowtie2-manual \
-		${DESTDIR}${PREFIX}/bin
 	(cd ${WRKSRC}/example && pax -rw index reads reference \
 		${DESTDIR}${EXAMPLESDIR})
 	(cd ${WRKSRC}/doc && pax -rw * ${DESTDIR}${DOCSDIR})
diff --git a/bowtie2/PLIST b/bowtie2/PLIST
index 71aaa407f1..b6d250260e 100644
--- a/bowtie2/PLIST
+++ b/bowtie2/PLIST
@@ -8,7 +8,6 @@ bin/bowtie2-build-s
 bin/bowtie2-inspect
 bin/bowtie2-inspect-l
 bin/bowtie2-inspect-s
-bin/bowtie2-manual
 share/bowtie2/scripts/bowtie2-hbb.sh
 share/bowtie2/scripts/convert_quals.pl
 share/bowtie2/scripts/gen_2b_occ_lookup.pl
diff --git a/bowtie2/files/bowtie2-manual b/bowtie2/files/bowtie2-manual
deleted file mode 100644
index 65f05a018e..0000000000
--- a/bowtie2/files/bowtie2-manual
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-webbrowser file:///usr/local/share/doc/bowtie/manual.html
-