Augustus
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Gaius-Augustus
Install augustus from source without root privileges
Since installing augustus from source without root previleges wasn't easy for me, I thought posting here the commands I used for installation.
-
If not already done, install conda, bioconda, and, optional but recommended, mamba (these are useful anyway).
-
Create and activate a dedicated environment for augustus (or activate an existing one of your choice):
conda create --yes --name augustus
conda activate augustus
- Write the list of dependencies to file
requirements.txtand install them:
echo "zlib
boost-cpp
gsl
htslib
lp_solve
biopython
perl
perl-app-cpanminus
perl-module-build
perl-yaml
perl-dbi
perl-scalar-list-utils
perl-file-which
perl-parallel-forkmanager
sqlite
suitesparse
cdbtools
diamond
ucsc-fatotwobit
ucsc-twobitinfo
bamtools
tar" > requirements.txt
mamba install --yes --file requirements.txt # or `conda install`
- Get the latest source code of augustus:
git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus
- Edit
common.mkwith the correct settings:
git checkout common.mk # Reset to original before editing it
> common.tmp
echo "
INCLUDE_PATH_ZLIB := -I${CONDA_PREFIX}/include
INCLUDE_PATH_BOOST := -I${CONDA_PREFIX}/include
INCLUDE_PATH_LPSOLVE := -I${CONDA_PREFIX}/include/lpsolve
INCLUDE_PATH_SUITESPARSE := -I${CONDA_PREFIX}/include/suitesparse/
INCLUDE_PATH_GSL := -I${CONDA_PREFIX}/include
INCLUDE_PATH_SQLITE := -I${CONDA_PREFIX}/include
INCLUDE_PATH_BAMTOOLS := -I${CONDA_PREFIX}/include/bamtools
INCLUDE_PATH_HTSLIB := -I${CONDA_PREFIX}/include/htslib
INCLUDE_PATH_SEQLIB := -I ${CONDA_PREFIX}/include/SeqLib -I${CONDA_PREFIX}/include/htslib -I${CONDA_PREFIX}/include/jsoncpp
LIBRARY_PATH_LPSOLVE := -L${CONDA_PREFIX}/lib/lp_solve/ -Wl,-rpath,${CONDA_PREFIX}/lib/lp_solve/
LIBRARY_PATH_ZLIB := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_BOOST := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_SUITESPARSE := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_GSL := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_SQLITE := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_BAMTOOLS := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_HTSLIB := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
LIBRARY_PATH_SEQLIB := -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib
" >> common.tmp
cat common.mk >> common.tmp
mv common.tmp common.mk
- Compile augustus and the auxiliary programs:
make MYSQL=false augustus auxprogs
echo $? # Check 0 exit code
- Copy the executables, scripts, and configs to the root directory of the conda environment:
mv bin/* ${CONDA_PREFIX}/bin/
cp -r scripts/* ${CONDA_PREFIX}/bin/
mkdir -p ${CONDA_PREFIX}/config
cp -r config/* ${CONDA_PREFIX}/config/
# Some basic tests:
augustus --version
autoAug.pl --help
- Before using augustus set the relevant variables:
export AUGUSTUS_CONFIG_PATH=${CONDA_PREFIX}/config/
export AUGUSTUS_SCRIPTS_PATH=${CONDA_PREFIX}/bin/
export AUGUSTUS_BIN_PATH=${CONDA_PREFIX}/bin/
Tested (not thoroughly) on Ubuntu 18 and CentOS 7 with augustus commit d1fd097. Note that augustus is also on bioconda but the version there may be outdated. Any feedback most welcome.
Thank you! This worked for me and saved me hours of pain. If our paths ever cross, I owe you a beer.
Hi, thanks for this, super useful! :)
I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory
I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams.* libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1
any advice on how to fix this?
You could try a softlink with the required file name. However, it might produce a segmentation fault. But it’s worth a try.
AnneJRomero @.***> schrieb am Do. 8. Sept. 2022 um 10:48:
Hi, thanks for this, super useful! :)
I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory
I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams.* libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1
any advice on how to fix this?
— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1240418418, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
You could try a softlink with the required file name. However, it might produce a segmentation fault. But it’s worth a try. AnneJRomero @.> schrieb am Do. 8. Sept. 2022 um 10:48: … Hi, thanks for this, super useful! :) I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams. libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1 any advice on how to fix this? — Reply to this email directly, view it on GitHub <#358 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA . You are receiving this because you are subscribed to this thread.Message ID: @.*>
Hi, I tried that and I'm still getting the same error message.
That’s weird. If the links are in the correct place, C++ programs usually try to use the files.
AnneJRomero @.***> schrieb am Do. 8. Sept. 2022 um 11:13:
You could try a softlink with the required file name. However, it might produce a segmentation fault. But it’s worth a try. AnneJRomero @.
*> schrieb am Do. 8. Sept. 2022 um 10:48: … <#m_-7890995221488165899_> Hi, thanks for this, super useful! :) I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams. libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1 any advice on how to fix this? — Reply to this email directly, view it on GitHub <#358 (comment) https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1240418418>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA . You are receiving this because you are subscribed to this thread.Message ID: @.**>
Hi, I tried that and I'm still getting the same error message.
— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1240446697, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JCYWRMEZAGBULWGYGTV5GU3TANCNFSM57DTKYAA . You are receiving this because you commented.Message ID: @.***>
Hi, I'm retrying again.
For the step, 'Compile augustus and the auxiliary programs':
make MYSQL=false augustus auxprogs echo $? # Check 0 exit code
I get the error:
mkdir -p bin
cd src && make
make[1]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/src' echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE" > cxxflags make[1]: Leaving directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/src'
mkdir -p bin
cd auxprogs && make
make[1]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs' cd aln2wig; make; make[2]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/aln2wig'
make[2]: aln2wig' is up to date. make[2]: Leaving directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/aln2wig'
cd bam2hints; make;
make[2]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/bam2hints' g++ -Wall -O3 -L/scratch/ar14g12/.conda/envs/augustus/lib -Wl,-rpath,/scratch/ar14g12/.conda/envs/augustus/lib -L/scratch/ar14g12/.conda/envs/augustus/lib -Wl,-rpath,/scratch/ar14g12/.conda/envs/augustus/lib -I/scratch/ar14g12/.conda/envs/augustus/include/bamtools -I/scratch/ar14g12/.conda/envs/augustus/include -o bam2hints bam2hints.o -lbamtools -lz bam2hints.o: In function main':
bam2hints.cc:(.text.startup+0x73e): undefined reference to BamTools::BamReader::Open(std::string const&)' collect2: error: ld returned 1 exit status make[2]: *** [bam2hints] Error 1 make[2]: Leaving directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/bam2hints'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs'
make: *** [auxprogs] Error 2
2
What am I doing wrong?
@AnneJRomero Can you start from a fresh conda environment, show the commands you execute with their output?
If it helps, on my setup libboost_iostreams.so is a symlink to libboost_iostreams.so.1.80.0:
conda activate augustus
ls -l ${CONDA_PREFIX}/lib/libboost_iostreams.so
lrwxrwxrwx 1 db291g db291g 28 Aug 20 18:42 /export/projects/III-data/wcmp_bioinformatics/db291g/miniconda3/envs/augustus/lib/libboost_iostreams.so -> libboost_iostreams.so.1.80.0
and this is my conda environment:
conda list
# packages in environment at /export/projects/III-data/wcmp_bioinformatics/db291g/miniconda3/envs/augustus:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bamtools 2.5.2 hd03093a_0 bioconda
biopython 1.79 py310h5764c6d_2 conda-forge
boost-cpp 1.80.0 h75c5d50_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cdbtools 0.99 hd03093a_7 bioconda
diamond 0.9.19 h2e03b76_5 bioconda
gmp 6.2.1 h58526e2_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
htslib 1.15.1 h9753748_0 bioconda
icu 70.1 h27087fc_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnghttp2 1.47.0 hdcd2b5c_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_1 conda-forge
libpng 1.6.37 h753d276_4 conda-forge
libsqlite 3.39.2 h753d276_1 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
lp_solve 5.5.2.5 h14c3975_1001 conda-forge
metis 5.1.0 h58526e2_1006 conda-forge
mpfr 4.1.0 h9202a9a_1 conda-forge
mysql-connector-c 6.1.11 h6eb9d5d_1007 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.23.2 py310h53a5b5f_0 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
perl-apache-test 1.43 pl5321hd8ed1ab_0 conda-forge
perl-app-cpanminus 1.7046 pl5321hd8ed1ab_0 conda-forge
perl-base 2.23 pl5321hdfd78af_2 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-class-load 0.25 pl5321hdfd78af_1 bioconda
perl-class-load-xs 0.10 pl5321h9f5acd7_6 bioconda
perl-class-method-modifiers 2.13 pl5321hdfd78af_0 bioconda
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-cpan-meta 2.150010 pl5321hdfd78af_1 bioconda
perl-cpan-meta-requirements 2.140 pl5321hdfd78af_1 bioconda
perl-cpan-meta-yaml 0.018 pl5321hdfd78af_1 bioconda
perl-data-dumper 2.183 pl5321h166bdaf_0 conda-forge
perl-data-optlist 0.112 pl5321hdfd78af_0 bioconda
perl-dbi 1.643 pl5321hec16e2b_1 bioconda
perl-devel-globaldestruction 0.14 pl5321hdfd78af_1 bioconda
perl-devel-overloadinfo 0.007 pl5321hdfd78af_0 bioconda
perl-devel-stacktrace 2.04 pl5321hdfd78af_1 bioconda
perl-dist-checkconflicts 0.11 pl5321hdfd78af_3 bioconda
perl-encode 3.19 pl5321hec16e2b_1 bioconda
perl-eval-closure 0.14 pl5321h9f5acd7_6 bioconda
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-extutils-cbuilder 0.280230 pl5321hdfd78af_2 bioconda
perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge
perl-extutils-manifest 1.73 pl5321hdfd78af_0 bioconda
perl-extutils-parsexs 3.44 pl5321hdfd78af_0 bioconda
perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge
perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge
perl-file-which 1.24 pl5321hd8ed1ab_0 conda-forge
perl-getopt-long 2.52 pl5321hdfd78af_0 bioconda
perl-ipc-cmd 1.04 pl5321hdfd78af_0 bioconda
perl-json-pp 4.11 pl5321hd8ed1ab_0 conda-forge
perl-locale-maketext-simple 0.21 pl5321hdfd78af_3 bioconda
perl-module-build 0.4231 pl5321hdfd78af_0 bioconda
perl-module-corelist 5.20220620 pl5321hdfd78af_0 bioconda
perl-module-implementation 0.09 pl5321hdfd78af_3 bioconda
perl-module-load 0.34 pl5321hdfd78af_0 bioconda
perl-module-load-conditional 0.68 pl5321hdfd78af_3 bioconda
perl-module-metadata 1.000037 pl5321hdfd78af_0 bioconda
perl-module-runtime 0.016 pl5321hdfd78af_2 bioconda
perl-module-runtime-conflicts 0.003 pl5321hdfd78af_1 bioconda
perl-moo 2.005004 pl5321hdfd78af_0 bioconda
perl-moose 2.2201 pl5321hec16e2b_2 bioconda
perl-mro-compat 0.15 pl5321hdfd78af_0 bioconda
perl-package-deprecationmanager 0.17 pl5321hdfd78af_1 bioconda
perl-package-stash 0.40 pl5321h87f3376_1 bioconda
perl-package-stash-xs 0.29 pl5321h87f3376_1 bioconda
perl-parallel-forkmanager 2.02 pl5321hdfd78af_1 bioconda
perl-params-check 0.38 pl5321hdfd78af_2 bioconda
perl-params-util 1.102 pl5321h9f5acd7_1 bioconda
perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-perl-ostype 1.010 pl5321hd8ed1ab_0 conda-forge
perl-role-tiny 2.002004 pl5321hdfd78af_0 bioconda
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-sub-exporter 0.988 pl5321hdfd78af_0 bioconda
perl-sub-exporter-progressive 0.001013 pl5321hdfd78af_1 bioconda
perl-sub-identify 0.14 pl5321hec16e2b_2 bioconda
perl-sub-install 0.928 pl5321hdfd78af_3 bioconda
perl-sub-name 0.21 pl5321hec16e2b_3 bioconda
perl-sub-quote 2.006006 pl5321hdfd78af_0 bioconda
perl-text-abbrev 1.02 pl5321hdfd78af_1 bioconda
perl-text-parsewords 3.31 pl5321hdfd78af_0 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-version 0.9929 pl5321h166bdaf_0 conda-forge
perl-xsloader 0.24 pl5321hd8ed1ab_0 conda-forge
perl-yaml 1.30 pl5321hdfd78af_0 bioconda
pip 22.2.2 pyhd8ed1ab_0 conda-forge
python 3.10.5 h582c2e5_0_cpython conda-forge
python_abi 3.10 2_cp310 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
setuptools 65.1.0 py310hff52083_0 conda-forge
sqlite 3.39.2 h4ff8645_1 conda-forge
suitesparse 5.10.1 h9e50725_1 conda-forge
tar 1.34 ha1f6473_0 conda-forge
tbb 2021.5.0 h924138e_1 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022c h191b570_0 conda-forge
ucsc-fatotwobit 377 ha8a8165_5 bioconda
ucsc-twobitinfo 377 ha8a8165_3 bioconda
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 h6239696_4 conda-forge
Hi,
I copied your list of packages, installed ones that I didn't have and updated the packages that were outdated.
I'm not getting the error message anymore. : $ augustus --version AUGUSTUS (3.4.0) is a gene prediction tool. Sources and documentation at https://github.com/Gaius-Augustus/Augustus
Thank you! :)
I tried testing the installation with: $ augustus --species=human --UTR=on examples/example.fa Segmentation fault (core dumped)
Why am I getting 'Segmentation fault (core dumped)' error?
I had the same problem as AnneJRomero. For some reason I couldn't install the same package versions as listed by dario using conda. For me, the only way to make a compiled augustus and auxprogs to work was to follow the install.md instructions (install every dependencies manually and point them in common.mk). Mysql++-dev without root it seens nearly impossible to do it, so use MYSQL=false argument as pointed by Dario. It surprised me that such a popular predictor is this hard to install... I really appreciate Dario's initiative to make it easier.
