sra-tools: NCBI's toolkit for Sequence Read Archives

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: sra-tools: NCBI's toolkit for Sequence Read Archives
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 12 Aug 2023 16:39:08 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Aug 12 11:39:08 2023 -0500
Changeset:	7ecb3482e356358cf6934cd2e9d4419fc9bbd5fe

Modified Files:
	Makefile
Added Files:
	sra-tools/DESCR
	sra-tools/Makefile
	sra-tools/PLIST
	sra-tools/distinfo
	sra-tools/distinfo.6155

Log Message:
sra-tools: NCBI's toolkit for Sequence Read Archives

SRA tools is a toolkit for using data in the INSDC Sequence Read
Archives.  SRAs operated by International Nucleotide Sequence Database
Collaboration houses sequence reads and alignments generated by
"next-gen" sequencers.  SRA tools allows conversion of .sra files, which
INSDC SRAs maintain, from/to other formats that the 'next-gen'
sequenecers generate including:

* csfasta/csqual (ABI SOLiD)
* fastq (and fasta for writing)
* hdf5 (PacBio, reading only)
* qseq (older Illumina)
* sam (writing only) / bam (reading only)
* sff

The toolkit uses NCBI-VDB back-end enabling seamless access to remote
SRA data and local SRA files.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7ecb3482e356358cf6934cd2e9d4419fc9bbd5fe

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

diffstat:
 Makefile                |  1 +
 sra-tools/DESCR         | 16 +++++++++
 sra-tools/Makefile      | 93 +++++++++++++++++++++++++++++++++++++++++++++++++
 sra-tools/PLIST         |  1 +
 sra-tools/distinfo      |  8 +++++
 sra-tools/distinfo.6155 |  0
 6 files changed, 119 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index a4a7dffc53..df22c380d7 100644
--- a/Makefile
+++ b/Makefile
@@ -5306,6 +5306,7 @@ SUBDIR+=	squirrelmail-avelsieve
 SUBDIR+=	squirrelmail-chg_sasl_passwd
 SUBDIR+=	squirrelmail-compatibility
 SUBDIR+=	squirrelmail-vlogin
+SUBDIR+=	sra-tools
 SUBDIR+=	src
 SUBDIR+=	srecord
 SUBDIR+=	srvx
diff --git a/sra-tools/DESCR b/sra-tools/DESCR
new file mode 100644
index 0000000000..b69fa774fb
--- /dev/null
+++ b/sra-tools/DESCR
@@ -0,0 +1,16 @@
+SRA tools is a toolkit for using data in the INSDC Sequence Read
+Archives.  SRAs operated by International Nucleotide Sequence Database
+Collaboration houses sequence reads and alignments generated by
+"next-gen" sequencers.  SRA tools allows conversion of .sra files, which
+INSDC SRAs maintain, from/to other formats that the 'next-gen'
+sequenecers generate including:
+
+* csfasta/csqual (ABI SOLiD)
+* fastq (and fasta for writing)
+* hdf5 (PacBio, reading only)
+* qseq (older Illumina)
+* sam (writing only) / bam (reading only)
+* sff
+
+The toolkit uses NCBI-VDB back-end enabling seamless access to remote
+SRA data and local SRA files.
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
new file mode 100644
index 0000000000..9dc1375b52
--- /dev/null
+++ b/sra-tools/Makefile
@@ -0,0 +1,93 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Sat Aug 12 11:25:27 CDT 2023               #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+#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
+#JAVA_VERSION=	17+
+#OPTIONS_DEFINE=	EXAMPLES
+#SHEBANG_GLOB=	*.sh
+
+DISTNAME=	sra-tools-3.0.6
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_TAG=	50f8b65d775f183ea3a179ba5650789a44697a25
+GITHUB_SUBMODULES+=	outpaddling ncbi-vdb 6da72e8 vdb/ncbi-vdb
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/ncbi/sra-tools
+COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
+# Check this
+LICENSE=	public-domain
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+# Upstream explicitly supports specific platforms
+ONLY_FOR_PLATFORM=	 *-*-aarch64 *-*-x86_64
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	bison cmake
+
+# The config.c and file-path.posix.cpp reinplaces follow
+# static patches.  Run "make clean patch" before updating
+# those patches so this reinplace does not get added to them.
+SUBST_CLASSES+=		etcdir
+SUBST_STAGE.etcdir=	pre-configure
+SUBST_SED.etcdir+=	-e 's|"/etc/ncbi"|"${PREFIX}/etc/ncbi"|g'
+SUBST_FILES.etcdir+=	${WRKSRC}/ncbi-vdb/libs/kfg/config.c
+
+SUBST_CLASSES+=		binpath
+SUBST_STAGE.binpath=	pre-configure
+SUBST_SED.binpath+=	-e 's|/usr/local/bin|${PREFIX}/bin|g'
+SUBST_FILES.binpath+=	${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
+
+SUBST_CLASSES+=		submoddir
+SUBST_STAGE.submoddir=	pre-configure
+SUBST_SED.submoddir+=	-e 's|/../ncbi-vdb|/ncbi-vdb|g'
+SUBST_FILES.submoddir+=	${WRKSRC}/CMakeLists.txt
+
+# FreeBSD's SHEBANG_FILES may include bash, perl, python, etc.
+# I don't know which is which, so you'll have to finish.
+# Add bash, etc. to USE_TOOLS if used below.
+# 
+REPLACE_SH=	*.sh
+
+USE_CMAKE=	yes
+# Check this
+CMAKE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
+
+pre-configure:
+	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
+
+post-install:
+	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${DISTVERSION}
+	${MV} ${DESTDIR}${PREFIX}/share/examples ${DESTDIR}${PREFIX}/share/examples-sratools
+	${MKDIR} ${DESTDIR}${EXAMPLESDIR}
+	${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}
+	${RMDIR} ${DESTDIR}${PREFIX}/share/examples-sratools
+	${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"
+# 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/PLIST b/sra-tools/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/sra-tools/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
new file mode 100644
index 0000000000..b3500bb889
--- /dev/null
+++ b/sra-tools/distinfo
@@ -0,0 +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
diff --git a/sra-tools/distinfo.6155 b/sra-tools/distinfo.6155
new file mode 100644
index 0000000000..e69de29bb2
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