Ubuntu
sra-sdk package

sra-sdk 3.0.3+dfsg-5ubuntu1 source package in Ubuntu

Changelog

sra-sdk (3.0.3+dfsg-5ubuntu1) mantic; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

sra-sdk (3.0.3+dfsg-5) unstable; urgency=medium

  * Limit libngs-java to those architectures where libs are available
    Closes: #1031853
  * DEP3 for all patches

 -- Steve Langasek <email address hidden>  Tue, 02 May 2023 12:58:30 +0200

Upload details

Uploaded by:
Steve Langasek
Uploaded to:
Mantic
Original maintainer:
Ubuntu Developers
Architectures:
amd64 arm64 all
Section:
science
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section

Builds

Mantic: [FULLYBUILT] amd64 [FULLYBUILT] arm64

Downloads

File Size SHA-256 Checksum
sra-sdk_3.0.3+dfsg.orig.tar.xz 30.3 MiB 1849cf932d6ec5c03577c184af7e286f6f5b9469ac1066d5a795fd02c9d842bc
sra-sdk_3.0.3+dfsg-5ubuntu1.debian.tar.xz 3.6 MiB 52ec18736ef34bd750a32f3a2deb2186e5c5d93650c806d1b0eaff6c9e6b1206
sra-sdk_3.0.3+dfsg-5ubuntu1.dsc 3.0 KiB 6803855f4404c98bb3bd576d582d7a0a9b4d2424e0d880cccfe6b6157ea70ba7

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