Skip to content

Latest commit

 

History

History
151 lines (126 loc) · 3.01 KB

DEPENDENCIES.md

File metadata and controls

151 lines (126 loc) · 3.01 KB
Raw

Extended pipeline dependencies

The extended pipeline depends on the following software. We list the recommended and tested versions for each release of taxator-tk starting from v1.3.3

Note, that the versions that can be installed via package manager in recent Linux distributions may differ and may be incompatible. For this reason, and to be most reproducible, I recommend to install the exact versions listed below, which are also containted in the binary extended release package.

If you use a different setup, please report all program versions with your results.

[1.5.0]

taxator-tk

Files: core binaries License: GPLv3 Link: https://github.com/fungs/taxator-tk/ Version: 1.5.0 Included: yes

NCBI BLAST+

Files: blastn, makeblastdb License: public domain software Link: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Version: 2.11.0+ Included: no

LAST

Files: lastal, lastdb, last-merge-batches License: GPLv3 Link: http://last.cbrc.jp Version: 1170 Included: no

GNU parallel

Files: parallel License: GPLv3 Link: http://www.gnu.org/software/parallel/ Version: 20201222 Included: yes

OrfM

Files: orfm License: LGPLv3 Link: https://github.com/wwood/OrfM Version: 0.7.1 Included: yes

KronaTools

Files: ktImportText, ktGetLibPath License: KRONA™ open-source license Link: https://github.com/marbl/Krona Version: 2.7.1 Included: no

LZ4

Files: lz4 License: BSD and GPLv2 Link: https://github.com/lz4/lz4/ Version: 1.9.3 Included: no

[1.4.0]

taxator-tk

Files: core binaries License: GPLv3 Link: https://github.com/fungs/taxator-tk/ Version: 1.4.0 Included: yes

NCBI BLAST+

Files: blastn, makeblastdb License: public domain software Link: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Version: 2.11.0+ Included: no

LAST

Files: lastal, lastdb, last-merge-batches License: GPLv3 Link: http://last.cbrc.jp Version: 1170 Included: no

GNU parallel

Files: parallel License: GPLv3 Link: http://www.gnu.org/software/parallel/ Version: 20201222 Included: yes

KronaTools

Files: ktImportText, ktGetLibPath License: KRONA™ open-source license Link: https://github.com/marbl/Krona Version: 2.7.1 Included: yes

LZ4

Files: lz4 License: BSD and GPLv2 Link: https://github.com/lz4/lz4/ Version: 1.9.3 Included: no

[1.3.3]

taxator-tk

Files: core binaries License: GPLv3 Link: https://github.com/fungs/taxator-tk/ Version: 1.3.3 Included: yes

NCBI BLAST+

Files: blastn, makeblastdb License: public domain software Link: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ Version: 2.2.28+ Included: no

LAST

Files: lastal, lastdb, last-merge-batches License: GPLv3 Link: http://last.cbrc.jp Version: 545 Included: no

GNU parallel

Files: parallel License: GPLv3 Link: http://www.gnu.org/software/parallel/ Version: 20150307 Included: yes

KronaTools

Files: ktImportText, ktGetLibPath License: KRONA™ open-source license Link: http://krona.sourceforge.net/ Version: 2.4 Included: yes

LZ4

Files: lz4 License: BSD and GPLv2 Link: https://github.com/lz4/lz4/ Version: r126 Included: no