sra-tools: Progress toward successful build

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Aug 12 18:55:58 2023 -0500
Changeset:	453126fd374e9cdd1a1a2e70ad67297a7b9ff738

Modified Files:
	sra-tools/Makefile
	sra-tools/distinfo

Log Message:
sra-tools: Progress toward successful build

Add deps, patch shebangs properly

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=453126fd374e9cdd1a1a2e70ad67297a7b9ff738

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

diffstat:
 sra-tools/Makefile | 28 +++++++++++-----------------
 sra-tools/distinfo | 12 ++++++------
 2 files changed, 17 insertions(+), 23 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 9dc1375b52..1c9157f081 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -11,24 +11,16 @@
 #LICENSE_COMB=		multi
 #LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 #LICENSE_DISTFILES_LGPL21+ =
-## Untested on other platforms, aarch64 support was recently added upstream
-# BUILD_DEPENDS=	bash:shells/bash
-# LIB_DEPENDS=	libxml2.so:textproc/libxml2 \
-#		libhdf5.so:science/hdf5 \
-#		libepoll-shim.so:devel/libepoll-shim \
-#		libzstd.so:archivers/zstd
 #USE_LDCONFIG=	${PREFIX}/lib64
 #USE_JAVA=	yes
-## Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
+# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
 #JAVA_VERSION=	17+
-#OPTIONS_DEFINE=	EXAMPLES
-#SHEBANG_GLOB=	*.sh
 
 DISTNAME=	sra-tools-3.0.6
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_TAG=	50f8b65d775f183ea3a179ba5650789a44697a25
-GITHUB_SUBMODULES+=	outpaddling ncbi-vdb 6da72e8 vdb/ncbi-vdb
+GITHUB_TAG=	de3d50d111874171766fd017c8cbcf92a9009263
+GITHUB_SUBMODULES+=	outpaddling ncbi-vdb 802ae6e ncbi-vdb
 
 OWNER=		bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/ncbi/sra-tools
@@ -40,11 +32,11 @@ LICENSE=	public-domain
 # MAKE_JOBS_SAFE=	no
 
 # Upstream explicitly supports specific platforms
+# Untested on other platforms, aarch64 support was recently added upstream
 ONLY_FOR_PLATFORM=	 *-*-aarch64 *-*-x86_64
 
-# Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
-USE_TOOLS+=	bison cmake
+USE_TOOLS+=	bash bison cmake
 
 # The config.c and file-path.posix.cpp reinplaces follow
 # static patches.  Run "make clean patch" before updating
@@ -67,8 +59,7 @@ SUBST_FILES.submoddir+=	${WRKSRC}/CMakeLists.txt
 # FreeBSD's SHEBANG_FILES may include bash, perl, python, etc.
 # I don't know which is which, so you'll have to finish.
 # Add bash, etc. to USE_TOOLS if used below.
-# 
-REPLACE_SH=	*.sh
+REPLACE_BASH=	*/*.sh */*/*.sh */*/*/*.sh
 
 USE_CMAKE=	yes
 # Check this
@@ -86,8 +77,11 @@ post-install:
 	${MV} ${DESTDIR}${PREFIX}/share/examples-java ${DESTDIR}${EXAMPLESDIR}/java
 	${MV} ${DESTDIR}${PREFIX}/share/examples-python ${DESTDIR}${EXAMPLESDIR}/python
 
-# Convert any _DEPENDS above that have a buildlink3.mk
-# .include "../..///buildlink3.mk"
+.include "../../textproc/libxml2/buildlink3.mk"
+.include "../../devel/hdf5/buildlink3.mk"
+.include "../../devel/libepoll-shim/buildlink3.mk"
+.include "../../archivers/zstd/buildlink3.mk"
+.include "../../devel/cmake/build.mk"
 # CentOS doesn't have zlib in the base, so uncomment if needed.
 # .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index b3500bb889..a5ef546e1a 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -1,8 +1,8 @@
 $NetBSD$
 
-BLAKE2s (outpaddling-ncbi-vdb-6da72e8.tar.gz) = 580cd0be2ff2edd656368866971a8927807e067c29b1618590e8d1ab6a7a9ffb
-SHA512 (outpaddling-ncbi-vdb-6da72e8.tar.gz) = a1e25168696ac8767cbc1cbc05c89bad6f610711f25d5e6499c6590027ff7638500422ba18301a5716e2cbe3b16de529016e0ee9abfa95166b42f12f7a8626ed
-Size (outpaddling-ncbi-vdb-6da72e8.tar.gz) = 18977770 bytes
-BLAKE2s (sra-tools-3.0.6-50f8b65d775f183ea3a179ba5650789a44697a25.tar.gz) = b35c89ecaceedfc34ec044ebc2990f69e24c80eadfacb498401779155c4e4315
-SHA512 (sra-tools-3.0.6-50f8b65d775f183ea3a179ba5650789a44697a25.tar.gz) = 572f25e3fe815805555ab5dd94ce249f2de205e5c4af3ce82ee07cd58bf75d48e7753eabd18773da6cddf628a9626a1a2d552714173c0d1701b1c7794668790c
-Size (sra-tools-3.0.6-50f8b65d775f183ea3a179ba5650789a44697a25.tar.gz) = 44961625 bytes
+BLAKE2s (outpaddling-ncbi-vdb-802ae6e.tar.gz) = bfdf236363008fb286611002e3997a9f8ac9277375de22dd0ec40222bbd117a3
+SHA512 (outpaddling-ncbi-vdb-802ae6e.tar.gz) = 5cb1f2c17fda873ba6c5fe24424dda72d596452ec15baf85870b9dad969a63448218551a637aa72313cf51543a2a89bdc55aa4066534f84fc9f7246f7cf0b6f3
+Size (outpaddling-ncbi-vdb-802ae6e.tar.gz) = 18977582 bytes
+BLAKE2s (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = b1d07bd7eedb1ca76f18e2715570ad52ac93af4999f48629f65a837566b7ead8
+SHA512 (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = 1286b69d45b111155152f2431e0bfa358519bb00fa0d1f78b437f16d8ea35d3d8ef7fb43280246c3142511a2b9118f3591aca7753648d8b22f375427adccf34c
+Size (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = 44963316 bytes