BSD Portsbiology/augustus 3.5.0_18 FreeBSD
Genome annotation tool
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
97a84ef467- License
- GPLv3
- Categories
- biology, science
- Package size
- 24776.2 KiB, 157607.9 KiB installed
Description
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
AUGUSTUS usually belongs to the most accurate programs for the species it is trained for. Often it is the most accurate ab initio program. For example, at the independent gene finder assessment (EGASP) on the human ENCODE regions AUGUSTUS was the most accurate gene finder among the tested ab initio programs. At the more recent nGASP (worm), it was among the best in the ab initio and transcript-based categories. See accuracy statistics for further details.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/augustus | 3.5.0_18 |
| HardenedBSD | biology/augustus | 3.5.0_18 |
| GhostBSD | biology/augustus | 3.5.0_17 |
Install
Binary package:
pkg install augustus-gene-predictionFrom the ports tree:
cd /usr/ports/biology/augustus/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= augustus-gene-prediction>0:biology/augustusPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 3.5.0_18 | 3.5.0_18 | - | - | - |
| FreeBSD:14:quarterly | 3.5.0_18 | 3.5.0_18 | n/a | - | - |
| FreeBSD:15:latest | 3.5.0_18 | 3.5.0_18 | n/a | - | 3.5.0_15 |
| FreeBSD:15:quarterly | 3.5.0_18 | 3.5.0_18 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.5.0_18 | 3.5.0_18 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 7
libbamtools.so: biology/bamtoolslibboost_iostreams.so: devel/boost-libslibcolamd.so: math/suitesparse-colamdlibgsl.so: math/gsllibhts.so: biology/htslibliblpsolve55.so: math/lp_solvelibmysqlpp.so: databases/mysql++
Runtime 1
samtools: biology/samtools
The full lists below include those, and their dependencies in turn.
Build dependencies 49
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/bamtools
- biology/htslib
- converters/libiconv
- databases/mysql++
- databases/mysql84-client
- databases/openldap26-client
- databases/sqlite3
- devel/binutils
- devel/boost-libs
- devel/gettext-runtime
- devel/gmake
- devel/icu
- devel/jsoncpp
- devel/libcbor
- devel/libedit
- devel/libffi
- devel/libunistring
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/gcc14
- lang/perl5.42
- lang/python312
- lang/tcl86
- math/gmp
- math/gsl
- math/libtommath
- math/lp_solve
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/suitesparse-colamd
- math/suitesparse-config
- print/indexinfo
- print/libpaper
- print/psutils
- security/cyrus-sasl2
- security/libfido2
- security/libssh2
- textproc/expat2
- textproc/groff
- textproc/uchardet
- www/libnghttp2
Run dependencies 49
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/bamtools
- biology/htslib
- biology/samtools
- converters/libiconv
- databases/mysql++
- databases/mysql84-client
- databases/openldap26-client
- databases/sqlite3
- devel/binutils
- devel/boost-libs
- devel/gettext-runtime
- devel/icu
- devel/jsoncpp
- devel/libcbor
- devel/libedit
- devel/libffi
- devel/libunistring
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/gcc14
- lang/perl5.42
- lang/python312
- lang/tcl86
- math/gmp
- math/gsl
- math/libtommath
- math/lp_solve
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/suitesparse-colamd
- math/suitesparse-config
- print/indexinfo
- print/libpaper
- print/psutils
- security/cyrus-sasl2
- security/libfido2
- security/libssh2
- textproc/expat2
- textproc/groff
- textproc/uchardet
- www/libnghttp2
No port depends on this one.
Configuration
No options to configure.
- USES
- gmake localbase:ldflags mysql perl5 python sqlite shebangfix
- Service scripts
- none
Files
pkg-plist 1523
- augustus/bin/aln2wig
- augustus/bin/augustus
- augustus/bin/bam2hints
- augustus/bin/bam2wig
- augustus/bin/compileSpliceCands
- augustus/bin/etraining
- augustus/bin/fastBlockSearch
- augustus/bin/filterBam
- augustus/bin/getSeq
- augustus/bin/homGeneMapping
- augustus/bin/joingenes
- augustus/bin/load2db
- augustus/bin/load2sqlitedb
- augustus/bin/pp_simScore
- augustus/bin/prepareAlign
- augustus/config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg
- augustus/config/cgp/log_reg_parameters_arabidopsis.cfg
- augustus/config/cgp/log_reg_parameters_default.cfg
- augustus/config/cgp/log_reg_parameters_fly.cfg
- augustus/config/cgp/log_reg_parameters_human.cfg
- augustus/config/cgp/log_reg_parameters_primates.cfg
- augustus/config/cgp/log_reg_parameters_s_aureus.cfg
- augustus/config/extrinsic/extrinsic-cgp.cfg
- augustus/config/extrinsic/extrinsic.E.XNT.cfg
- augustus/config/extrinsic/extrinsic.E.cfg
- augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg
- augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg
- augustus/config/extrinsic/extrinsic.M.RM.PB.cfg
- augustus/config/extrinsic/extrinsic.ME.cfg
- augustus/config/extrinsic/extrinsic.MEMS.cfg
- augustus/config/extrinsic/extrinsic.MP.cfg
- augustus/config/extrinsic/extrinsic.MPE.cfg
- augustus/config/extrinsic/extrinsic.MT.cfg
- augustus/config/extrinsic/extrinsic.cfg
- augustus/config/model/constraints_shadow_partial.txt
- augustus/config/model/constraints_shadow_partial_utr.txt
- augustus/config/model/ovlp_len.pbl
- augustus/config/model/ovlp_len_archaea.pbl
- augustus/config/model/states_shadow.cfg
- augustus/config/model/states_shadow_2igenic.cfg
- augustus/config/model/states_shadow_bacterium.cfg
- augustus/config/model/states_shadow_intronless.cfg
- augustus/config/model/states_shadow_utr.cfg
- augustus/config/model/states_shadow_utr_nc.cfg
- augustus/config/model/states_singlestrand.cfg
- augustus/config/model/states_singlestrand_2igenic.cfg
- augustus/config/model/trans_shadow_atleastone.pbl
- augustus/config/model/trans_shadow_bacterium.pbl
- augustus/config/model/trans_shadow_complete.pbl
- augustus/config/model/trans_shadow_complete_utr.pbl
- augustus/config/model/trans_shadow_exactlyone.pbl
- augustus/config/model/trans_shadow_intronless.pbl
- augustus/config/model/trans_shadow_partial.pbl
- augustus/config/model/trans_shadow_partial_utr.pbl
- augustus/config/model/trans_shadow_partial_utr_nc.pbl
- augustus/config/model/trans_singlestrand_atleastone.pbl
- augustus/config/model/trans_singlestrand_complete.pbl
- augustus/config/model/trans_singlestrand_exactlyone.pbl
- augustus/config/model/trans_singlestrand_partial.pbl
- augustus/config/parameters/AUG_CMDLN_PARAMETERS.md
- augustus/config/parameters/aug_cmdln_parameters.json
- augustus/config/profile/blosum55.qij
- augustus/config/profile/blosum62.qij
- augustus/config/profile/default.qij
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg
- augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt
- augustus/config/species/Anopheles_gambiae/README.txt
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg
- augustus/config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt
- augustus/config/species/Argopecten_irradians/README.txt
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg
- augustus/config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt
- augustus/config/species/Aurelia_aurita/README.txt
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg
- augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt
- augustus/config/species/Bathycoccus_prasinos/README.txt
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz | 2.2591893e+08 | 5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686 |