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EvolBioInf / fur

Find Unique genomic Regions
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Issues on esa #16

Open xy-repo opened 9 months ago

xy-repo commented 9 months ago

Dear author,

When building the bin file "makeFurDB", there is an error "package github.com/evolbioinf/esa: build constraints exclude all Go files in /home/xiayao/tools/fur/makeFurDb/esa". I do not have root access. Is there anyway to solve this problem?

Thanks for your time.

haubold commented 9 months ago

I'm a bit surprised that your directory fur/makeFurDb contains the subdirectory esa. That shouldn't be the case. What happens if you go into /home/xiayao/tools, remove the current fur, clone it again, and then make the programs?

cd ~/tools/fur rm -rf fur git clone https://github.com/evolbioinf/fur cd fur make

xy-repo commented 9 months ago

Thank you for your reply. The folder "esa" was manually placed into that folder. I have tried numerous ways to compile makeFurDB, including make it from scratch. However, the issue remains the same: "build constraints exclude all Go files in 'esa'." Since I don't have root access, I am installing all dependencies under the conda environment. Is there a way for users without root access to compile it? Perhaps you could provide information about the versions of gcc, g++, Go, libc, etc.?

haubold commented 9 months ago

Unfortunately, I don't know how to compile Fur under conda. But can you run the docker container mentioned in the README? That might be a way to get started.

xy-repo commented 9 months ago

The docker also need the root access to install. Thank you anyway.

wangzhichao1990 commented 8 months ago

Thank you for your reply. The folder "esa" was manually placed into that folder. I have tried numerous ways to compile makeFurDB, including make it from scratch. However, the issue remains the same: "build constraints exclude all Go files in 'esa'." Since I don't have root access, I am installing all dependencies under the conda environment. Is there a way for users without root access to compile it? Perhaps you could provide information about the versions of gcc, g++, Go, libc, etc.?

Compiling and installing this software is indeed very difficult, especially on older operating systems. I am using CentOS 7, so I used Conda to install the compilation tools. The env yaml is displayed as follows :

name: toolchain
channels:
  - https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
  - https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _go_select=2.3.0=cgo
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_13
  - alsa-lib=1.2.10=hd590300_0
  - atk-1.0=2.38.0=hd4edc92_1
  - attr=2.5.1=h166bdaf_1
  - autoconf=2.71=pl5321h2b4cb7a_1
  - automake=1.16.5=pl5321ha770c72_0
  - binutils=2.40=hdd6e379_0
  - binutils_impl_linux-64=2.40=hf600244_0
  - binutils_linux-64=2.40=hbdbef99_2
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.20.1=hd590300_0
  - c-compiler=1.6.0=hd590300_0
  - ca-certificates=2023.7.22=hbcca054_0
  - cairo=1.18.0=h3faef2a_0
  - chrpath=0.16=h7f98852_1002
  - cmake=3.27.6=hcfe8598_0
  - compilers=1.6.0=ha770c72_0
  - cxx-compiler=1.6.0=h00ab1b0_0
  - dbus=1.13.6=h5008d03_3
  - expat=2.5.0=hcb278e6_1
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=hab24e00_0
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fortran-compiler=1.6.0=heb67821_0
  - freetype=2.12.1=h267a509_2
  - fribidi=1.0.10=h36c2ea0_0
  - gcc=12.3.0=h8d2909c_2
  - gcc_impl_linux-64=12.3.0=he2b93b0_2
  - gcc_linux-64=12.3.0=h76fc315_2
  - gdk-pixbuf=2.42.10=h829c605_4
  - gettext=0.21.1=h27087fc_0
  - gfortran=12.3.0=h499e0f7_2
  - gfortran_impl_linux-64=12.3.0=hfcedea8_2
  - gfortran_linux-64=12.3.0=h7fe76b4_2
  - giflib=5.2.1=h0b41bf4_3
  - glib=2.78.0=hfc55251_0
  - glib-tools=2.78.0=hfc55251_0
  - gnuplot=5.4.8=h142138f_0
  - go=1.21.3=h4d9269f_0
  - graphite2=1.3.13=h58526e2_1001
  - gsl=2.7=he838d99_0
  - gst-plugins-base=1.22.6=h8e1006c_2
  - gstreamer=1.22.6=h98fc4e7_2
  - gtk2=2.24.33=h90689f9_2
  - gxx=12.3.0=h8d2909c_2
  - gxx_impl_linux-64=12.3.0=he2b93b0_2
  - gxx_linux-64=12.3.0=h8a814eb_2
  - harfbuzz=8.2.1=h3d44ed6_0
  - icu=73.2=h59595ed_0
  - kernel-headers_linux-64=3.10.0=h4a8ded7_13
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.21.2=h659d440_0
  - lame=3.100=h166bdaf_1003
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libblas=3.9.0=19_linux64_openblas
  - libcap=2.69=h0f662aa_0
  - libcblas=3.9.0=19_linux64_openblas
  - libclang=15.0.7=default_h7634d5b_3
  - libclang13=15.0.7=default_h9986a30_3
  - libcups=2.3.3=h4637d8d_4
  - libcurl=8.4.0=hca28451_0
  - libdeflate=1.19=hd590300_0
  - libdivsufsort=2.0.2=h031d066_8
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libevent=2.1.12=hf998b51_1
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libflac=1.4.3=h59595ed_0
  - libgcc-devel_linux-64=12.3.0=h8bca6fd_2
  - libgcc-ng=13.2.0=h807b86a_2
  - libgcrypt=1.10.1=h166bdaf_0
  - libgd=2.3.3=h119a65a_9
  - libgfortran-ng=13.2.0=h69a702a_2
  - libgfortran5=13.2.0=ha4646dd_2
  - libglib=2.78.0=hebfc3b9_0
  - libgomp=13.2.0=h807b86a_2
  - libgpg-error=1.47=h71f35ed_0
  - libiconv=1.17=h166bdaf_0
  - libjpeg-turbo=3.0.0=hd590300_1
  - libllvm15=15.0.7=h5cf9203_3
  - libnghttp2=1.52.0=h61bc06f_0
  - libnsl=2.0.1=hd590300_0
  - libogg=1.3.4=h7f98852_1
  - libopenblas=0.3.24=pthreads_h413a1c8_0
  - libopus=1.3.1=h7f98852_1
  - libpng=1.6.39=h753d276_0
  - libpq=16.0=hfc447b1_1
  - libsanitizer=12.3.0=h0f45ef3_2
  - libsndfile=1.2.2=hc60ed4a_1
  - libsqlite=3.43.2=h2797004_0
  - libssh2=1.11.0=h0841786_0
  - libstdcxx-devel_linux-64=12.3.0=h8bca6fd_2
  - libstdcxx-ng=13.2.0=h7e041cc_2
  - libsystemd0=254=h3516f8a_0
  - libtiff=4.6.0=ha9c0a0a_2
  - libuuid=2.38.1=h0b41bf4_0
  - libuv=1.46.0=hd590300_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp=1.3.2=h658648e_1
  - libwebp-base=1.3.2=hd590300_0
  - libxcb=1.15=h0b41bf4_0
  - libxkbcommon=1.6.0=h5d7e998_0
  - libxml2=2.11.5=h232c23b_1
  - libzlib=1.2.13=hd590300_5
  - lz4-c=1.9.4=hcb278e6_0
  - m4=1.4.18=h516909a_1001
  - make=4.3=hd18ef5c_1
  - mpg123=1.32.3=h59595ed_0
  - mysql-common=8.0.33=hf1915f5_5
  - mysql-libs=8.0.33=hca2cd23_5
  - ncurses=6.4=hcb278e6_0
  - nspr=4.35=h27087fc_0
  - nss=3.94=h1d7d5a4_0
  - openssl=3.1.3=hd590300_0
  - pango=1.50.14=ha41ecd1_2
  - pcre2=10.40=hc3806b6_0
  - perl=5.32.1=4_hd590300_perl5
  - pip=23.3=pyhd8ed1ab_0
  - pixman=0.42.2=h59595ed_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - pulseaudio-client=16.1=hb77b528_5
  - python=3.12.0=hab00c5b_0_cpython
  - qt-main=5.15.8=h82b777d_17
  - readline=8.2=h8228510_1
  - rhash=1.4.4=hd590300_0
  - sdsl-lite=2.1.1=h00ab1b0_1002
  - setuptools=68.2.2=pyhd8ed1ab_0
  - sysroot_linux-64=2.17=h4a8ded7_13
  - tk=8.6.13=h2797004_0
  - tzdata=2023c=h71feb2d_0
  - wheel=0.41.2=pyhd8ed1ab_0
  - xcb-util=0.4.0=hd590300_1
  - xcb-util-image=0.4.0=h8ee46fc_1
  - xcb-util-keysyms=0.4.0=h8ee46fc_1
  - xcb-util-renderutil=0.3.9=hd590300_1
  - xcb-util-wm=0.4.1=h8ee46fc_1
  - xkeyboard-config=2.40=hd590300_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.1.1=hd590300_0
  - xorg-libsm=1.2.4=h7391055_0
  - xorg-libx11=1.8.7=h8ee46fc_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-libxt=1.3.0=hd590300_1
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.5.5=hfc55251_0

Additionally, you need to install Noweb separately.

haubold commented 1 month ago

It's been a while, but I have now removed the dependency on Noweb. Thank you for pointing out this problem.