Source: sra-sdk Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Aaron M. Ucko Section: science Priority: optional Build-Depends: debhelper-compat (= 13), cmake, d-shlibs, dh-python, javahelper, libncbi-vdb-dev (>= 3.0.1+dfsg~), libfuse-dev, libhdf5-dev, libmagic-dev, libre2-dev, libxml2-dev, libzstd-dev, liblzma-dev, libsam-extract-dev, markdown | libtext-markdown-perl | discount , maven-repo-helper, python3-all, python3-distutils, default-jdk, flex, bison Standards-Version: 4.6.2 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.