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 | Published | Component | Section |
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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 |
Available diffs
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