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Port details on branch 2022Q2
ncbi-vdb NCBI's virtualized back-end for accessing Sequence Read Archive
2.11.0_4 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.11.0_4Version of this port present on the latest quarterly branch.
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 2022-04-24 04:16:20
Last Update: 2022-04-10 19:47:23
Commit Hash: 035e778
License: PD
WWW:
https://github.com/ncbi/ncbi-vdb/wiki
Description:
NCBI-VDB is a virtualized back-end engine library for Sequencing Read Archives. The 'front-end' API are provided by biology/ngs-sdk port. Although the GitHub repository also contains Java and Python codes, this port currently builds only C- and C++-based libraries. WWW: https://github.com/ncbi/ncbi-vdb/wiki
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (39 items)
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  1. @ldconfig
  2. /usr/local/share/licenses/ncbi-vdb-2.11.0_4/catalog.mk
  3. /usr/local/share/licenses/ncbi-vdb-2.11.0_4/LICENSE
  4. /usr/local/share/licenses/ncbi-vdb-2.11.0_4/PD
  5. include/ncbi-vdb/NGS.hpp
  6. lib/libkdf5-static.a
  7. lib/libkdf5.a
  8. lib/libkdf5.a.2
  9. lib/libkdf5.a.2.11.0
  10. lib/libkdf5.so
  11. lib/libkdf5.so.2
  12. lib/libkdf5.so.2.11.0
  13. lib/libncbi-ngs-c++-static.a
  14. lib/libncbi-ngs-c++.a
  15. lib/libncbi-ngs-c++.a.2
  16. lib/libncbi-ngs-c++.a.2.11.0
  17. lib/libncbi-ngs-static.a
  18. lib/libncbi-ngs.a
  19. lib/libncbi-ngs.a.2
  20. lib/libncbi-ngs.a.2.11.0
  21. lib/libncbi-vdb-static.a
  22. lib/libncbi-vdb.a
  23. lib/libncbi-vdb.a.2
  24. lib/libncbi-vdb.a.2.11.0
  25. lib/libncbi-vdb.so
  26. lib/libncbi-vdb.so.2
  27. lib/libncbi-vdb.so.2.11.0
  28. lib/libncbi-wvdb-static.a
  29. lib/libncbi-wvdb.a
  30. lib/libncbi-wvdb.a.2
  31. lib/libncbi-wvdb.a.2.11.0
  32. lib/libncbi-wvdb.so
  33. lib/libncbi-wvdb.so.2
  34. lib/libncbi-wvdb.so.2.11.0
  35. lib/ncbi/certs.kfg
  36. lib/ncbi/default.kfg
  37. @owner
  38. @group
  39. @mode
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Dependency lines:
  • ncbi-vdb>0:biology/ncbi-vdb
To install the port:
cd /usr/ports/biology/ncbi-vdb/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ncbi-vdb
  • pkg install ncbi-vdb
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ncbi-vdb
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64 i386
distinfo:
TIMESTAMP = 1618218620 SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539

Expand this list (2 items)

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SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365

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No package information for this port in our database
Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link: pkg-fallout
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. libepoll-shim>0 : devel/libepoll-shim
  3. gmake>=4.3 : devel/gmake
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libxml2.so : textproc/libxml2
  2. libhdf5.so : science/hdf5
  3. libmbedtls.so : security/mbedtls
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_ncbi-vdb
USES:
compiler:c11 gmake localbase:ldflags perl5 shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ncbi/ncbi-vdb/tar.gz/2.11.0?dummy=/
Collapse this list.

Number of commits found: 1

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.11.0_4
10 Apr 2022 19:47:23
commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6commit hash: 035e778ee53345464c2d7466a3895e17073ad1f6 files touched by this commit		 Charlie Li (vishwin) search for other commits by this committer 
textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate and direct commit to quarterly as PORTREVISIONs
may not match from main.

PR: 262853, 262940, 262877
Approved by: fluffy (mentor)

Number of commits found: 1
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