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sra-sdk package

sra-sdk 3.0.3+dfsg-7ubuntu1 source package in Ubuntu

Changelog

sra-sdk (3.0.3+dfsg-7ubuntu1) oracular; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.
    - Drop build-dependency on python3-distutils, see #1065961

sra-sdk (3.0.3+dfsg-7) unstable; urgency=medium

  * debian/control: Build depend on libabsl-dev so binaries using libre2
    (sharq and relevant tests) can unconditionally link against
    -labsl_string_view for simplicitly.
  * debian/patches/support_libre2-11.patch (new): Prepare for (but don't
    require!) newer libre2 versions where re2::StringPiece has changed
    from a custom class to a typedef for absl::string_view, whose API is
    somewhat different.  (Closes: #1053411.)

 -- Gianfranco Costamagna <email address hidden>  Fri, 24 May 2024 22:09:26 +0200

Upload details

Uploaded by:
Gianfranco Costamagna
Uploaded to:
Oracular
Original maintainer:
Debian Med
Architectures:
amd64 arm64 all
Section:
science
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section

Builds

Oracular: [FULLYBUILT] amd64 [FULLYBUILT] arm64

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File Size SHA-256 Checksum
sra-sdk_3.0.3+dfsg.orig.tar.xz 30.3 MiB 1849cf932d6ec5c03577c184af7e286f6f5b9469ac1066d5a795fd02c9d842bc
sra-sdk_3.0.3+dfsg-7ubuntu1.debian.tar.xz 3.6 MiB f4b35703f129021a90765f0c1e00f21f8ebd3671eb87fec2e40127d4705adcae
sra-sdk_3.0.3+dfsg-7ubuntu1.dsc 2.8 KiB 9a69985b169536a8eb411b34074530a00aaeed9b28d5138d089be06675ed8105

View changes file

Binary packages built by this source

libncbi-ngs-dev: Next Generation Sequencing language Bindings (C++ development)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.
 .
 This is the full development package.

libncbi-ngs3: Next Generation Sequencing language Bindings (full runtime)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.

libncbi-ngs3-dbgsym: debug symbols for libncbi-ngs3
libngs-c++-dev: Next Generation Sequencing language Bindings (C++ development)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.
 .
 This is the development package for C++ usage.

libngs-c++3: Next Generation Sequencing language Bindings (C++ runtime)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.

libngs-c++3-dbgsym: debug symbols for libngs-c++3
libngs-java: Next Generation Sequencing language Bindings (Java bindings)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.
 .
 Java bindings.

libngs-java-doc: Next Generation Sequencing language Bindings (Java documentation)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.
 .
 Documentation for the Java bindings.

libngs-jni: Next Generation Sequencing language Bindings (Java native binding)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.
 .
 Java native bindings.

python3-ngs: Next Generation Sequencing language Bindings (Python3 bindings)

 NGS is a new, domain-specific API for accessing reads, alignments and
 pileups produced from Next Generation Sequencing. The API itself is
 independent from any particular back-end implementation, and supports
 use of multiple back-ends simultaneously. It also provides a library for
 building new back-end "engines". The engine for accessing SRA data is
 contained within the sister repository ncbi-vdb.
 .
 The API is currently expressed in C++, Java and Python languages. The
 design makes it possible to maintain a high degree of similarity between
 the code in one language and code in another - especially between C++
 and Java.
 .
 Python3 bindings.

sra-toolkit: utilities for the NCBI Sequence Read Archive

 Tools for reading the SRA archive, generally by converting individual runs
 into some commonly used format such as fastq.
 .
 The textual dumpers "sra-dump" and "vdb-dump" are provided in this
 release as an aid in visual inspection. It is likely that their
 actual output formatting will be changed in the near future to a
 stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON
 THE OUTPUT FORMAT SEEN IN THIS RELEASE.
 .
 Other tools distributed in this package are:
  abi-dump, abi-load
  align-info
  bam-load
  cache-mgr
  cg-load
  copycat
  fasterq-dump
  fastq-dump, fastq-load
  helicos-load
  illumina-dump, illumina-load
  kar
  kdbmeta
  latf-load
  pacbio-load
  prefetch
  rcexplain
  remote-fuser
  sff-dump, sff-load
  sra-pileup, sra-sort, sra-stat, srapath
  srf-load
  test-sra
  vdb-config, vdb-copy, vdb-decrypt, vdb-encrypt, vdb-get, vdb-lock,
  vdb-passwd, vdb-unlock, vdb-validate
 .
 The "help" information will be improved in near future releases, and
 the tool options will become standardized across the set. More documentation
 will also be provided documentation on the NCBI web site.
 .
 Tool options may change in the next release. Version 1 tool options
 will remain supported wherever possible in order to preserve
 operation of any existing scripts.

sra-toolkit-dbgsym: debug symbols for sra-toolkit