wiggletools.c -lcrypto needed for compilation.
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git clone https://github.com/dahlo/WiggleTools
cd WiggleTools
# make ... gives error below ... -lcrypto is missing from the cc command
# ~/biotools/WiggleTools/src$ cc -g -Wall -O3 -std=gnu99 -L../lib -L../../libBigWig -L../../htslib wiggletools.c -lwiggletools -l:libBigWig.a -lcurl -l:libhts.a -lgsl -lgslcblas -lz -lpthread -lm -llzma -lbz2 -o ../bin/wiggletools
# /usr/bin/ld: ../../htslib/libhts.a(hfile_s3.o): undefined reference to symbol 'EVP_sha256@@OPENSSL_3.0.0'
# /usr/bin/ld: /lib/x86_64-linux-gnu/libcrypto.so.3: error adding symbols: DSO missing from command line
# collect2: error: ld returned 1 exit status
# Do this instead ...
cd src
cc -g -Wall -O3 -std=gnu99 -L../lib -L../../libBigWig -L../../htslib wiggletools.c -lwiggletools -l:libBigWig.a -lcurl -l:libhts.a -lgsl -lgslcblas -lz -lpthread -lm -llzma -lbz2 -o ../bin/wiggletools -lcrypto
cd ..
Hi @marcovth
Thanks for flagging this up.
I tried to reproduce the error using the original Ensembl/WiggleTools code in a few Linux environments (Ubuntu 22.04, Debian 11, Rocky 8), but everything worked fine instead.
Apparently, the crypto library (and headers) is installed by default in these distributions or it comes with the development/building tools.
Did you use a different distro or OS?
I tried to translate this docker recipe into a singularity script ...
https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/blob/master/Dockerfile
But in the end, even with my adaptation, it crashed on WiggleTools
====
_BootStrap: docker
From: debian:latest
IncludeCmd: yes
sudo singularity build --notest ./CAT.singularity.sif ./CAT.singularity.def.txt
%post
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
this will install all necessary packages and prepare the container
apt-get -y update
apt-get -y upgrade
apt-get install -y build-essential libssl-dev libncurses5-dev libcurl4-openssl-dev liblzma-dev libbz2-dev
libboost-all-dev sqlite3 libsqlite3-0 libsqlite3-dev libgsl0-dev lp-solve liblpsolve55-dev libbamtools-dev wget git unzip
apt-get install -y libbz2-dev liblzma-dev libcurl4-openssl-dev pkg-config libncurses5-dev
apt-get -y install libboost-dev
mkdir /root/tools
cd /root/tools
htslib
wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2
tar -xvjf htslib-1.16.tar.bz2
mv htslib-1.16 htslib
cd htslib
./configure
make
make install
cd ..
rm ./htslib-1.16.tar.bz2
bcftools
wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2
tar -xvjf bcftools-1.16.tar.bz2
mv bcftools-1.16 bcftools
cd bcftools
./configure
make
make install
cd ..
rm ./bcftools-1.16.tar.bz2
samtools
wget https://github.com/samtools/samtools/releases/download/1.16/samtools-1.16.tar.bz2
tar -xvjf samtools-1.16.tar.bz2
mv samtools-1.16 samtools
cd samtools
./configure
make
make install
cd ..
rm ./samtools-1.16.tar.bz2
Augustus
apt-get update
apt-get install -y build-essential wget git autoconf
Install dependencies for AUGUSTUS comparative gene prediction mode (CGP)
apt-get install -y libgsl-dev libboost-all-dev libsuitesparse-dev liblpsolve55-dev
apt-get install -y libsqlite3-dev libmysql++-dev
Install dependencies for the optional support of gzip compressed input files
apt-get install -y libboost-iostreams-dev zlib1g-dev
Install dependencies for bam2hints and filterBam
apt-get install -y libbamtools-dev zlib1g-dev
Install additional dependencies for bam2wig
apt-get install -y samtools libhts-dev
Install additional dependencies for homGeneMapping and utrrnaseq
apt-get install -y libboost-all-dev
Install additional dependencies for scripts
apt-get install -y cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl libyaml-perl libdbd-mysql-perl
apt-get install -y --no-install-recommends python3-biopython
git clone https://github.com/Gaius-Augustus/Augustus augustus
cd augustus && git reset --hard ${AUGUSTUS_COMMIT}
echo 'COMPGENEPRED = true' >> ./common.mk
echo 'SQLITE = true' >> ./common.mk
cd ./auxprogs/homGeneMapping/src && sed 's/# BOOST = true/BOOST = true/g' -i Makefile && sed 's/# SQLITE = true/SQLITE = true/g' -i Makefile
cd ../../../
make
#make install
cd ..
HDF5
wget -q http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz
tar xzf hdf5-1.10.1.tar.gz
mv hdf5-1.10.1 hdf5
cd hdf5 && ./configure --enable-cxx --prefix=/usr
make
make install
cd ..
rm hdf5-1.10.1.tar.gz
sonLib
git clone https://github.com/ComparativeGenomicsToolkit/sonLib.git
cd sonLib
make
cd ..
HAL
git clone https://github.com/ComparativeGenomicsToolkit/hal.git
cd hal
make
#make install
cd ..
LibBigWig
git clone https://github.com/dpryan79/libBigWig.git
cd libBigWig
make
#make install
cd ..
WiggleTools
git clone https://github.com/dahlo/WiggleTools
ln -s /usr/bin/cc /bin/cc
cd WiggleTools
make ... gives error below ... -lcrypto is missing from the cc command !
~/biotools/WiggleTools/src$ cc -g -Wall -O3 -std=gnu99 -L../lib -L../../libBigWig -L../../htslib wiggletools.c -lwiggletools -l:libBigWig.a -lcurl -l:libhts.a -lgsl -lgslcblas -lz -lpthread -lm -llzma -lbz2 -o ../bin/wiggletools
/usr/bin/ld: ../../htslib/libhts.a(hfile_s3.o): undefined reference to symbol 'EVP_sha256@@OPENSSL_3.0.0'
/usr/bin/ld: /lib/x86_64-linux-gnu/libcrypto.so.3: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Do this instead ...
mkdir -p ./bin
cd src
cc -g -Wall -O3 -std=gnu99 -L../lib -L../../libBigWig -L../../htslib wiggletools.c -lwiggletools -l:libBigWig.a -lcurl -l:libhts.a -lgsl -lgslcblas -lz -lpthread -lm -llzma -lbz2 -o ../bin/wiggletools -lcrypto
cd ..
make
cd ..
sambamba
wget -q https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v0.6.7_linux.tar.bz2
tar xvjf sambamba_v0.6.7_linux.tar.bz2
rm ./sambamba_v0.6.7_linux.tar.bz2
apt-get update
apt-get install -y wget bedtools bamtools samtools sqlite3 libgsl0-dev libcolamd2 software-properties-common libcurl4-openssl-dev exonerate
add-apt-repository -y ppa:deadsnakes/ppa
apt-get install -y python3.7 python3-pip
for i in wigToBigWig faToTwoBit gff3ToGenePred genePredToBed genePredToFakePsl bamToPsl transMapPslToGenePred
pslPosTarget axtChain chainMergeSort pslMap pslRecalcMatch pslMapPostChain gtfToGenePred genePredToGtf bedtools
pslCheck pslCDnaFilter clusterGenes pslToBigPsl bedSort bedToBigBed; do
wget -q http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/$i -O /bin/$i ; chmod +x /bin/$i ; done
cp ./hal/bin/* /bin/
cp ./sambamba /bin/
cp ./augustus/bin/* /bin/
cp ./augustus/scripts/* /bin/
cp ./WiggleTools/bin/* /bin/
mkdir -p /augustus
cp /augustus/config /augustus/config
Python deps
pip3 install bd2k-python-lib toil[all]==5.0 pyfasta numpy matplotlib pandas==1.0
make Python 3 primary python
rm /usr/bin/python
ln -s /usr/bin/python3.7 /usr/bin/python
ENV AUGUSTUS_CONFIG_PATH=/augustus/config/_
Hello @marcovth - I have tried for since your message above, but could not reproduce the error; hence, unsure how to help.
I used Docker - not Singularity - and tried with ubuntu:20.04, bullseye, python:3.9-bullseye, and python:3.9-slime-bullseye. Also compiled samtools packages (htslib, bcftools, samtools) from both direct git clone and version-specific TAR archives.
In the end, I stumbled upon a few errors in the entire process of making the CAT Dockerfile work with Ubuntu 20.04 or Debian 11 ... but they seem to be more related to the multi-stage image building process "only", rather than real compatibility problems. And never stumbled upon the missing libcrypto error.
Also, abandoning any optimisation, I "translated" your steps above into yet another Dockerfile (started from python:3.9-bullseye). And - again - I could not get the "libcrypto" error.
Closing for now (not reproducible). @marcovth please feel free to reach out, should you need it.