Cannot find multiple dependencies

[FabianDK]

Hello,

Unfortunately I am getting errors during the installation when I type "make".

/usr/bin/ld: cannot find -llpsolve55 /usr/bin/ld: cannot find -lcolamd /usr/bin/ld: cannot find -lmysqlclient /usr/bin/ld: cannot find -lmysqlpp

I do not have this folder /usr/bin/ld.

Here is what I have done so far:

1. Installed mysql++-3.2.5 to folder mysql++_install
2. Downloaded lp_solve_5.5.2.5_dev_ux64
3. Changed Augustus/src/Makefile: Line 30: INCLS += -I/nfs/research1/a/b/Programs/lp_solve_5.5.2.5_dev_ux64 Line 40:RUNTIME_LIBPATH = -Wl,-rpath=/nfs/research1/a/b/Programs/mysql++_install/lib Line 41: INCLS += -I/usr/include/mysql -I/nfs/research1/a/b/Programs/mysql++_install/include/mysql++

Then after "make", I get this:

mkdir -p bin cd src && make make[1]: Entering directory `/nfs/research1/a/b/Programs/Augustus/src' g++ -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -DZIPINPUT -std=c++11 -DCOMPGENEPRED -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o sqliteDB.o dummy.o -I../include -I/nfs/research1/a/b/Programs/lp_solve_5.5.2.5_dev_ux64 -I/usr/include/mysql -I/nfs/research1/a/b/Programs/mysql++_install/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3

/usr/bin/ld: cannot find -llpsolve55 /usr/bin/ld: cannot find -lcolamd /usr/bin/ld: cannot find -lmysqlclient /usr/bin/ld: cannot find -lmysqlpp collect2: error: ld returned 1 exit status make[1]: *** [augustus] Error 1 make[1]: Leaving directory `/nfs/research1/a/b/Programs/Augustus/src' make: *** [all] Error 2

I'd be grateful for your help.

[starling13]

Try to add -L/nfs/research1/a/b/Programs/mysql++_install/lib to LIBS variable at line 42.

/usr/bin/ld: cannot find -lmysqlclient

Are mysql development files installed? You may try to use pkg-config: LIBS += `pkg-config --libs mysqlclient` ... instead of LIBS += -lmysqlclient ...

I do not have this folder /usr/bin/ld

It's ok, ld is the executable of GNU linker and it works correctly at your host.

[FabianDK]

Unfortunately, this still gives the same error. I have downloaded mysql++-3.2.5 from the website and installed it with .configure, make, make install. All other required packages I have got through conda.

packages in environment at /homes/danfab/anaconda3/envs/test_aug:

Name Version Build Channel bamtools 2.5.1 he860b03_5 bioconda blas 1.0 mkl anaconda boost 1.71.0 py38_0 anaconda bzip2 1.0.8 h7b6447c_0 anaconda ca-certificates 2020.1.1 0
certifi 2019.11.28 py38_0
gsl 2.6 h294904e_0 conda-forge icu 58.2 h211956c_0 anaconda intel-openmp 2020.0 166 anaconda ld_impl_linux-64 2.33.1 h53a641e_7 anaconda libblas 3.8.0 14_mkl conda-forge libboost 1.71.0 h97c9712_0 anaconda libboost-dev 1.68.0 2748 statiskit libcblas 3.8.0 14_mkl conda-forge libedit 3.1.20181209 hc058e9b_0 anaconda libffi 3.2.1 h4deb6c0_3 anaconda libgcc-ng 9.1.0 hdf63c60_0 anaconda libgfortran-ng 7.3.0 hdf63c60_0 anaconda liblapack 3.8.0 14_mkl conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 anaconda lp_solve 5.5.2.5 h14c3975_1001 conda-forge lpsolve55 5.5 py38hc1659b7_1001 conda-forge metis 5.1.0 he1b5a44_1005 conda-forge mkl 2019.5 281 anaconda mkl-service 2.3.0 py38he904b0f_0 anaconda mkl_fft 1.0.15 py38ha843d7b_0 anaconda mkl_random 1.1.0 py38h962f231_0 anaconda ncurses 6.2 he6710b0_0 anaconda numpy 1.18.1 py38h4f9e942_0 anaconda numpy-base 1.18.1 py38hde5b4d6_1 anaconda openssl 1.1.1d h7b6447c_4
pip 20.0.2 py38_1 anaconda py-boost 1.71.0 py38h962f231_0 anaconda python 3.8.1 h0371630_1 anaconda readline 7.0 h7b6447c_5 anaconda setuptools 45.2.0 py38_0 anaconda six 1.14.0 py38_0 anaconda sqlite 3.31.1 h7b6447c_0 anaconda suitesparse 5.6.0 h717dc36_0 conda-forge tbb 2020.1 hc9558a2_0 conda-forge tk 8.6.8 hbc83047_0 anaconda wheel 0.34.2 py38_0 anaconda xz 5.2.4 h14c3975_4 anaconda yaml 0.1.7 had09818_2
zlib 1.2.11 h7b6447c_3 anaconda zstd 1.3.7 h0b5b093_0 anaconda

I also tried to install Augustus with "conda install -c bioconda augustus". It seems to work but when I type augustus in the terminal I get:

augustus: error while loading shared libraries: libboost_iostreams.so.1.60.0: cannot open shared object file: No such file or directory

In principle, my goal is to use BRAKER2. But I get this error after typing braker.pl -h.

Thu Mar 5 11:13:15 2020: Found environment variable $CDBTOOLS_PATH. Setting $CDBTOOLS_PATH to /nfs/research1/a/b/Programs/cdbfasta/ Thu Mar 5 11:13:15 2020: ERROR: in file /nfs/research1/a/bl/Programs/BRAKER/scripts/braker.pl at line 3323 /homes/danfab/anaconda3/envs/BRAKER/bin/../config/../bin/augustus not executable on this machine.

I guess the reason is that I could not install Augustus or that there is this libboost_iostreams.so.1.60.0 error?

[starling13]

At least the /usr/bin/ld: cannot find -lmysqlclient should be gone...

augustus: error while loading shared libraries: libboost_iostreams.so.1.60.0: cannot open shared object file: No such file or directory

libboost_iostreams is not installed or has different version?

[KatharinaHoff]

For BRAKER, you can download an older AUGUSTUS release that links ok with bioconda. Replace the scripts directory by the current AUGUSTUS scripts.

[starling13]

Unfortunately, this still gives the same error.

I sure this errors have simple solution. If the directory /nfs/research1/a/b/Programs/mysql++_install/lib contains *.so or *.a file of libmysql++.so..., and makefile variable LIBS contains the option -L/nfs/research1/a/b/Programs/mysql++_install/lib -lmysql++ option should work.

[FabianDK]

Many thanks for your replies. I think I got braker2 to run using @KatharinaHoff 's advice. This is what I had to do: I have managed to install Augustus 3.1 with

conda install -c bioconda augustus=3.1 The other versions gave the same libboost_iostreams.so.1.60.0 error.

However, braker then complained about the joingenes executable missing.

joingenes executable not found at /homes/danfab/anaconda3/envs/BRAKER/bin/../config/../bin/joingenes. Please compile joingenes (augustus/auxprogs/joingenes)!

I had to go into my git cloned Augustus folder (newest version), find auxprogs/joingenes and 'make'. Then I moved the joingenes executable to the bin folder in my anaconda environment.

Next I added the Anaconda/Augustus paths (scripts/config/bin) to my my bashrc.

After that braker2 could not find: filterGenesIn.pl, aa2nonred.pl, getAnnoFastaFromJoingenes.py, fix_joingenes_gtf.pl, fix_in_frame_stop_codon_genes.py. I moved those from my git cloned Augustus folder to my anaconda env scripts folder.

Now, braker.pl seems to be running. Thanks for the solutions.

[KatharinaHoff]

@MarioStanke We need to discuss how to improve compilation instructions for current AUGUSTUS release after CGP mode went into default. It causes problems for a large number of BRAKER users.

[starling13]

The least clear part of installation for me was lpsolve. Which distrbution to use and how to compile. I end up with making autotools build files by hands for a heap of sources, downloaded from sourceforge page of lpsolve.

[DustinSokolowski]

Hey @KatharinaHoff and @MarioStanke. I was wondering if this conversation ever happened and there's an easier solution than @FabianDK's? Otherwise I'll get started on this.

Also, would you expect that we'd need to install augustus through conda specifically for this bug fix to work?

Best, Dustin