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Source: sra-sdk
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Andreas Tille <tille@debian.org>,
Aaron M. Ucko <ucko@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
cmake,
d-shlibs,
dh-python,
javahelper,
libabsl-dev,
libncbi-vdb-dev (>= 3.2.1+dfsg~),
libhdf5-dev,
libmagic-dev,
libre2-dev,
libxml2-dev,
libzstd-dev,
liblzma-dev,
libsam-extract-dev,
maven-repo-helper,
python3-all,
python3-setuptools,
python3-vdb,
default-jdk,
flex,
bison
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/sra-sdk
Vcs-Git: https://salsa.debian.org/med-team/sra-sdk.git
Homepage: https://github.com/ncbi/sra-tools/
Rules-Requires-Root: no
Package: sra-toolkit
Architecture: amd64 arm64
Depends: ${shlibs:Depends},
${misc:Depends}
Recommends: med-config
Description: 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.
Package: libngs-c++3
Multi-Arch: same
Architecture: amd64 arm64
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
Description: 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.
Package: libngs-c++-dev
Multi-Arch: same
Architecture: amd64 arm64
Section: libdevel
Depends: ${misc:Depends},
libngs-c++3 (= ${binary:Version})
Breaks: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3)
Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3)
Description: 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.
Package: libncbi-ngs3
Multi-Arch: same
Architecture: amd64 arm64
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
Description: 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.
Package: libncbi-ngs-dev
Multi-Arch: same
Architecture: amd64 arm64
Section: libdevel
Depends: ${misc:Depends},
libncbi-ngs3 (= ${binary:Version}),
libngs-c++-dev (= ${binary:Version})
Description: 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.
Package: libngs-java
Multi-Arch: same
Architecture: amd64 arm64
Section: java
Depends: ${java:Depends},
${misc:Depends},
libngs-jni (>= ${source:Version}),
libngs-jni (<< ${source:Version}.1~)
Recommends: ${java:Recommends}
Suggests: libngs-java-doc
Description: 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.
Package: libngs-jni
Multi-Arch: same
Architecture: amd64 arm64
Section: java
Depends: ${shlibs:Depends},
libncbi-ngs3 (= ${binary:Version}),
${misc:Depends}
Description: 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.
Package: libngs-java-doc
Multi-Arch: foreign
Architecture: all
Section: doc
Depends: ${misc:Depends}
Description: 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.
Package: python3-ngs
Architecture: all
Section: python
Depends: ${python3:Depends},
${misc:Depends},
libncbi-ngs3 (>= ${source:Version}),
libncbi-ngs3 (<< ${source:Version}.1~)
Description: 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.
|
