Compiling error for missing header files

[lye2]

I am trying to build a docker image with the Dockerfile provided. But I am getting some errors for header files during the compiling process.

FastqReader.cpp:1:10: fatal error: SeqLib/FastqReader.h: No such file or directory
#include "SeqLib/FastqReader.h"
^~~~~~~~~~~~~~~~~~~~~~
BFC.cpp:33:10: fatal error: SeqLib/BFC.h: No such file or directory
#include "SeqLib/BFC.h"
^~~~~~~~~~~~~~
compilation terminated.
compilation terminated.
ReadFilter.cpp:1:10: fatal error: SeqLib/ReadFilter.h: No such file or directory
#include "SeqLib/ReadFilter.h"
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [libseqlib_a-BFC.o] Error 1
make[2]: *** Waiting for unfinished jobs....
SeqPlot.cpp:1:10: fatal error: SeqLib/SeqPlot.h: No such file or directory
#include "SeqLib/SeqPlot.h"
^~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:435: recipe for target 'libseqlib_a-BFC.o' failed
Makefile:449: recipe for target 'libseqlib_a-ReadFilter.o' failed
make[2]: *** [libseqlib_a-ReadFilter.o] Error 1
Makefile:421: recipe for target 'libseqlib_a-FastqReader.o' failed
make[2]: *** [libseqlib_a-FastqReader.o] Error 1
Makefile:463: recipe for target 'libseqlib_a-SeqPlot.o' failed
make[2]: *** [libseqlib_a-SeqPlot.o] Error 1
ssw_cpp.cpp:1:10: fatal error: SeqLib/ssw_cpp.h: No such file or directory
#include "SeqLib/ssw_cpp.h"
^~~~~~~~~~~~~~~~~~
compilation terminated.
RefGenome.cpp:1:10: fatal error: SeqLib/RefGenome.h: No such file or directory
#include "SeqLib/RefGenome.h"
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
GenomicRegion.cpp:1:10: fatal error: SeqLib/GenomicRegion.h: No such file or directory
#include "SeqLib/GenomicRegion.h"
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:477: recipe for target 'libseqlib_a-ssw_cpp.o' failed
make[2]: *** [libseqlib_a-ssw_cpp.o] Error 1
Makefile:505: recipe for target 'libseqlib_a-RefGenome.o' failed
make[2]: *** [libseqlib_a-RefGenome.o] Error 1
Makefile:491: recipe for target 'libseqlib_a-GenomicRegion.o' failed
make[2]: *** [libseqlib_a-GenomicRegion.o] Error 1
ssw.c:44:10: fatal error: SeqLib/ssw.h: No such file or directory
#include "SeqLib/ssw.h"
^~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [libseqlib_a-ssw.o] Error 1
Makefile:393: recipe for target 'libseqlib_a-ssw.o' failed
make[2]: Leaving directory '/svaba/SeqLib/src'
Makefile:358: recipe for target 'all-recursive' failed
make[1]: Leaving directory '/svaba'
make[1]: *** [all-recursive] Error 1
Makefile:299: recipe for target 'all' failed
make: *** [all] Error 2
The command '/bin/sh -c cd svaba && ./configure && make -j$(nproc) && make -j$(nproc) install' returned a non-zero code: 2

[walaj]

I'm not sure, it looks an issue with the include (-I) paths during the build. Can you show me any of the actual compilation lines?

…

On Thu, Oct 12, 2023 at 10:12 PM lye2 ***@***.***> wrote: I am trying to build a docker image with the Dockerfile provided. But I am getting some errors for header files during the compiling process. FastqReader.cpp:1:10: fatal error: SeqLib/FastqReader.h: No such file or directory #include "SeqLib/FastqReader.h" ^~~~~~~~~~~~~~~~~~~~~~ BFC.cpp:33:10: fatal error: SeqLib/BFC.h: No such file or directory #include "SeqLib/BFC.h" ^~~~~~~~~~~~~~ compilation terminated. compilation terminated. ReadFilter.cpp:1:10: fatal error: SeqLib/ReadFilter.h: No such file or directory #include "SeqLib/ReadFilter.h" ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [libseqlib_a-BFC.o] Error 1 make[2]: *** Waiting for unfinished jobs.... SeqPlot.cpp:1:10: fatal error: SeqLib/SeqPlot.h: No such file or directory #include "SeqLib/SeqPlot.h" ^~~~~~~~~~~~~~~~~~ compilation terminated. Makefile:435: recipe for target 'libseqlib_a-BFC.o' failed Makefile:449: recipe for target 'libseqlib_a-ReadFilter.o' failed make[2]: *** [libseqlib_a-ReadFilter.o] Error 1 Makefile:421: recipe for target 'libseqlib_a-FastqReader.o' failed make[2]: *** [libseqlib_a-FastqReader.o] Error 1 Makefile:463: recipe for target 'libseqlib_a-SeqPlot.o' failed make[2]: *** [libseqlib_a-SeqPlot.o] Error 1 ssw_cpp.cpp:1:10: fatal error: SeqLib/ssw_cpp.h: No such file or directory #include "SeqLib/ssw_cpp.h" ^~~~~~~~~~~~~~~~~~ compilation terminated. RefGenome.cpp:1:10: fatal error: SeqLib/RefGenome.h: No such file or directory #include "SeqLib/RefGenome.h" ^~~~~~~~~~~~~~~~~~~~ compilation terminated. GenomicRegion.cpp:1:10: fatal error: SeqLib/GenomicRegion.h: No such file or directory #include "SeqLib/GenomicRegion.h" ^~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. Makefile:477: recipe for target 'libseqlib_a-ssw_cpp.o' failed make[2]: *** [libseqlib_a-ssw_cpp.o] Error 1 Makefile:505: recipe for target 'libseqlib_a-RefGenome.o' failed make[2]: *** [libseqlib_a-RefGenome.o] Error 1 Makefile:491: recipe for target 'libseqlib_a-GenomicRegion.o' failed make[2]: *** [libseqlib_a-GenomicRegion.o] Error 1 ssw.c:44:10: fatal error: SeqLib/ssw.h: No such file or directory #include "SeqLib/ssw.h" ^~~~~~~~~~~~~~ compilation terminated. make[2]: *** [libseqlib_a-ssw.o] Error 1 Makefile:393: recipe for target 'libseqlib_a-ssw.o' failed make[2]: Leaving directory '/svaba/SeqLib/src' Makefile:358: recipe for target 'all-recursive' failed make[1]: Leaving directory '/svaba' make[1]: *** [all-recursive] Error 1 Makefile:299: recipe for target 'all' failed make: *** [all] Error 2 The command '/bin/sh -c cd svaba && ./configure && make -j$(nproc) && make -j$(nproc) install' returned a non-zero code: 2 — Reply to this email directly, view it on GitHub <#129>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUZ7CEAFIR63EMMT3B4RODX7CPR3ANCNFSM6AAAAAA56OU25Y> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lye2]

Here is the line above the error:
g++ -DHAVE_CONFIG_H -I. -I../.. -I../htslib -Wno-sign-compare -g -Wall -Wextra -Wno-unknown-pragmas -std=c++11 -D_GLIBCXX_USE_CXX11_ABI=0 -g -O2 -MT libseqlib_a-FastqReader.o -MD -MP -MF .deps/libseqlib_a-FastqReader.Tpo -c -o libseqlib_a-FastqReader.o test -f 'FastqReader.cpp' || echo './'FastqReader.cpp

[walaj]

I've been working on getting away from autotools and using cmake, I think time to implement now for this. I just updated the master branch to now use cmake. The issue is that the build now should point to a system htslib. Can you try this Dockerfile? I tested most of it, but it won't compile on apple silicon right now due to some dependencies in fermi-lite that haven't been updated yet

# Start with an Ubuntu image
FROM ubuntu:20.04

# Avoid prompts with tzdata (timezones)
ENV DEBIAN_FRONTEND=noninteractive

# Install dependencies for htslib and svaba
RUN apt update && apt install -y \
    autoconf \
    automake \
    make \
    gcc \
    g++ \
    git \
    perl \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libcurl4-gnutls-dev \
    libssl-dev \
    cmake \
    && rm -rf /var/lib/apt/lists/*

# Clone and install htslib
WORKDIR /opt
RUN git clone --recursive https://github.com/samtools/htslib.git && \
    cd htslib && \
    autoheader && \
    autoconf && \
    ./configure && \
    make && \
    make install

# Ensure shared libraries are noticed
RUN ldconfig

# Clone svaba
WORKDIR /opt
RUN git clone --recursive https://github.com/walaj/svaba.git && cd svaba && mkdir build

# Compile svaba with htslib
WORKDIR /opt/svaba/build
RUN cmake .. \
    -DHTSLIB_INCLUDE_DIR=/usr/local/include \
    -DHTSLIB_LIBRARY=/usr/local/lib/libhts.so && make

ENV PATH "$PATH:/svaba/build"

[lye2]

This worked for me. Thanks!