Ubuntu
ncbi-vdb package

ncbi-vdb 2.11.2+dfsg-3 source package in Ubuntu

Changelog

ncbi-vdb (2.11.2+dfsg-3) unstable; urgency=medium

  * Leave mbedtls quirk handling to d-shlibs (>= 0.104).  (Closes: #999788.)
  * Skip VDB3, at least for now -- it FTBFS on i386, and has so far just
    been an uninstalled technology preview.
  * Enable arm64 builds.  To that end:
    - add_-msse2.patch: Limit -msse2 to 32-bit x86.  (Redundant on 64-bit
      x86, invalid elsewhere.)
    - debian/rules: Wildcard upstream architecture name (VDB_ARCH), no
      longer consistently aligned with any single dpkg-architecture variable.
  * debian/watch: Track tags rather than releases, of which GitHub no
    longer lists any(!).

 -- Aaron M. Ucko <email address hidden>  Sat, 20 Nov 2021 23:06:09 -0500

Upload details

Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
amd64 arm64 i386 x32
Section:
misc
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section

Builds

Jammy: [FULLYBUILT] amd64 [FULLYBUILT] arm64

Downloads

File Size SHA-256 Checksum
ncbi-vdb_2.11.2+dfsg-3.dsc 2.7 KiB 102f63eec74ada4aa2066f38520bb5d7f10e01343f3a68d2464b90d1b179221d
ncbi-vdb_2.11.2+dfsg.orig.tar.xz 18.6 MiB 5b0dc693fe237f35c421f91bdbf04d718e9f1121ced2f7830d001b34cdaff15b
ncbi-vdb_2.11.2+dfsg-3.debian.tar.xz 21.4 KiB 7e2ad5a94003225053daf2fdc01c8af29df02454850e696826b04bff85be27ec

Available diffs

No changes file available.

Binary packages built by this source

libkdf5-2: hdf5 access to data in the INSDC Sequence Read Archives

 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.
 .
 This library is part of the ncbi-vdb package and provides an interface
 to the Hierarchical Data Format 5 (HDF5).

libkdf5-2-dbgsym: debug symbols for libkdf5-2
libkdf5-dev: hdf5 access to data in the INSDC Sequence Read Archives (devel)

 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.
 .
 This library is part of the ncbi-vdb package and provides an interface
 to the Hierarchical Data Format 5 (HDF5).
 .
 This is the development package.

libncbi-vdb-dev: libraries for using data in the INSDC Sequence Read Archives (devel)

 Much of the data submitted these days, for example in BAM, Illumina
 export.txt, and Complete Genomics formats, contain alignment
 information. With aligned data, NCBI uses Compression by Reference,
 which only stores the differences in base pairs between sequence data
 and the segment it aligns to. The process to restore original data, for
 example as FastQ, requires fast access to the reference sequences that
 the original data was aligned to. NCBI recommends that SRA users
 dedicate local disk space to store references downloaded from the NCBI
 SRA site. As of Fall 2014, the complete collection of these reference
 sequences is 66 GB. While it isn't usually necessary to download the
 entirety of the reference sequences, this should give you an idea of the
 scale of the storage requirement. By default, the Toolkit will download
 missing reference sequences on demand and cache them in the user's home
 directory. The location of this cache is configurable, as is whether the
 download is automatic or manual.
 .
 This is the development package.

libncbi-vdb2: libraries for using data in the INSDC Sequence Read Archives

 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-vdb2-dbgsym: debug symbols for libncbi-vdb2
libncbi-wvdb-dev: virtual layer update modul of ncbi-vdb library (devel)

 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.
 .
 This library is part of the ncbi-vdb package.
 .
 This is the development package.

libncbi-wvdb2: virtual layer update modul of ncbi-vdb library

 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.
 .
 This library is part of the ncbi-vdb package.

libncbi-wvdb2-dbgsym: debug symbols for libncbi-wvdb2
libvdb-sqlite-dev: sqlite modul of ncbi-vdb library (devel)

 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.
 .
 This library is part of the ncbi-vdb package and provides a sqlite
 interface.
 .
 This is the development package.

libvdb-sqlite2: sqlite modul of ncbi-vdb library

 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.
 .
 This library is part of the ncbi-vdb package and provides a sqlite
 interface.

libvdb-sqlite2-dbgsym: debug symbols for libvdb-sqlite2