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cpouchon / REFMAKER

Make your own nuclear references from genomic assemblies of shotgun libraries.
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Installation error on Ubuntu #1

Closed jmhallas closed 4 months ago

jmhallas commented 10 months ago

Hello,

I am trying to install REFMAKER on an Ubuntu 16.04.7 LTS (GNU/Linux 4.15.0-142-generic x86_64) using the following code.

wget https://github.com/cpouchon/REFMAKER/archive/master.zip

unzip master.zip

rm master.zip

cd ./REFMAKER-main

source /share/cdfwwildlife/hallas_dedicated/Miniconda/etc/profile.d/conda.sh

conda env create --prefix /share/cdfwwildlife/hallas_dedicated/Miniconda/envs/refmaker-env --file /share/cdfwwildlife/hallas_dedicated/programs/REFMAKER-main/env/refmaker-env.yml

This is the error I receive:

Retrieving notices: ...working... done
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:
  - openjdk==17.0.3=hbc0c0cd_4
  - libxslt==1.1.33=h320ff13_0
  - libedit==3.1.20191231=h0678c8f_2
  - bzip2==1.0.8=h0d85af4_4
  - spades==3.15.2=he641558_0
  - perl-list-moreutils-xs==0.430=pl5321ha5712d3_1
  - pcre2==10.40=h1c4e4bc_0
  - libunistring==0.9.10=h0d85af4_0
  - scipy==1.5.3=py36h4f136de_1
  - entrez-direct==16.2=h193322a_1
  - libzlib==1.2.13=hfd90126_4
  - cutadapt==1.18=py36h1de35cc_1
  - tornado==6.1=py36hfa26744_1
  - openssl==1.1.1s=hfd90126_0
  - libcurl==7.86.0=h57eb407_1
  - dbus==1.13.6=h811a1a6_3
  - sqlite==3.37.0=h23a322b_0
  - perl-compress-raw-bzip2==2.201=pl5321h9722bc1_0
  - perl-pathtools==3.75=pl5321ha5712d3_3
  - htslib==1.13=hc38c3fb_0
  - gsl==2.6=h71c5fe9_2
  - perl==5.32.1=2_h0d85af4_perl5
  - lxml==4.6.3=py36habcf893_0
  - libpng==1.6.39=ha978bb4_0
  - xz==5.2.6=h775f41a_0
  - gettext==0.21.1=h8a4c099_0
  - perl-scalar-list-utils==1.62=pl5321ha5712d3_0
  - libidn2==2.3.4=hb7f2c08_0
  - libtiff==4.0.9=h79f4b77_1002
  - krb5==1.19.3=hb49756b_0
  - setuptools==49.6.0=py36h79c6626_3
  - trimal==1.4.1=hcd10b59_6
  - libopenblas==0.3.21=openmp_h429af6e_3
  - icu==64.2=h6de7cb9_1
  - libcxx==14.0.6=hccf4f1f_0
  - libblas==3.9.0=16_osx64_openblas
  - libxml2==2.9.10=h53d96d6_0
  - libsqlite==3.40.0=ha978bb4_0
  - perl-io-compress==2.201=pl5321h9722bc1_0
  - wget==1.20.3=h52ee1ee_1
  - libssh2==1.10.0=h7535e13_3
  - matplotlib-base==3.2.2=py36h83d3ec1_1
  - expat==2.5.0=hf0c8a7f_0
  - perl-json-xs==2.34=pl5321hcd10b59_5
  - libgfortran==5.0.0=9_5_0_h97931a8_26
  - tk==8.6.12=h5dbffcc_0
  - ncurses==6.2=h2e338ed_4
  - bcftools==1.13=h450d709_0
  - pcre==8.45=he49afe7_0
  - qt==5.9.7=h8cf7e54_3
  - scikit-learn==0.24.2=py36h979b75d_1
  - python==3.6.15=haf480d7_0_cpython
  - libffi==3.4.2=h0d85af4_5
  - liblapack==3.9.0=16_osx64_openblas
  - perl-compress-raw-zlib==2.105=pl5321h9722bc1_0
  - pyqt==5.9.2=py36h2a560b1_4
  - curl==7.86.0=h57eb407_1
  - c-ares==1.18.1=h0d85af4_0
  - libgcc==4.8.5=1
  - libglib==2.74.1=h4c723e1_1
  - libdeflate==1.7=h35c211d_5
  - jpeg==9e=hac89ed1_2
  - cd-hit==4.8.1=h10c929f_7
  - mafft==7.508=ha5712d3_0
  - libcblas==3.9.0=16_osx64_openblas
  - bwa==0.7.17=h1f540d2_9
  - ca-certificates==2022.9.24=h033912b_0
  - certifi==2021.5.30=py36h79c6626_0
  - llvm-openmp==15.0.5=h61d9ccf_0
  - freetype==2.12.1=h3f81eb7_0
  - sip==4.19.8=py36h0a44026_1000
  - samtools==1.13=h7596a89_0
  - libnghttp2==1.47.0=h7cbc4dc_1
  - numpy==1.19.5=py36h08b5fde_2
  - readline==8.1=h05e3726_0
  - pigz==2.6=h5dbffcc_0
  - libgfortran5==11.3.0=h082f757_26
  - libiconv==1.17=hac89ed1_0
  - blast==2.12.0=h0370960_3
  - kiwisolver==1.3.1=py36hc61eee1_1
  - r-base==3.3.1=0
  - biopython==1.78=py36h9ed2024_0
  - libev==4.33=haf1e3a3_1
  - zlib==1.2.13=hfd90126_4
  - perl-encode==3.19=pl5321ha5712d3_1

I have tried installing the program in different locations but still receive the same error. I have looked for examples of this error and one explanation I found was there might be an issue with an Ubuntu. I am able to use the same code and load the programs onto my personal Macbook pro laptop, which makes me believe there is a possible compatibility issue with the HPC.

Any advice or suggestions would be greatly appreciated.

Thank you for your time and advice,

Joshua Hallas

cpouchon commented 10 months ago

Hi Joshua,

It is an issue with the installation file on your system. I need to change this on the main page.

You have to install the dependencies within your environment using these lines:

1) create the environment:

conda create --name /share/cdfwwildlife/hallas_dedicated/Miniconda/envs/refmaker-env

2) load the environement:

conda activate /share/cdfwwildlife/hallas_dedicated/Miniconda/envs/refmaker-env

3) and now install the dependencies

conda install python picard">=2.27" bwa markov_clustering scipy matplotlib networkx spades blast mafft trimal numpy joblib bwa cd-hit ete3 biopython samtools">=1.13" bcftools">=1.13" -y

Tell me if you have any issues

Best regards,

Charles

bombnattanon commented 9 months ago

Hi Charles,

I had the same issue as Joshua. I was also trying to create the refmaker environment in Unix. Perhaps, when you export the conda environment, try using the --no-builds command. I am not sure if it might help broaden the dependency search.

I did try to manually remove the build versions from your refmaker-env.yml file. I used the modified .yml file above to create a new environment though. It still didn't work but the error seems to be reduced now.

Encountered problems while solving:
  - nothing provides requested libgfortran 5.0.0**
  - nothing provides icu 54.* needed by r-base-3.3.1-1
  - nothing provides system needed by clangdev-4.0.0-default_0
  - package openjdk-17.0.3-h1e1ecb3_1 requires harfbuzz >=5.1.0,<6.0a0, but none of the providers can be installed
  - package htslib-1.13-h9093b5e_0 requires libcurl >=7.77.0,<8.0a0, but none of the providers can be installed

However, after installing all the dependencies you provided above manually, it seemed to work! Then, I exported my refmaker-env environment using the flag "--no-builds" and tested it by creating a new environment using this .yml file and it seemed to work (at least for my machine).

name: refmaker-env
channels:
  - smirarab
  - conda-forge
  - bioconda
  - defaults
  - r
dependencies:
  - _libgcc_mutex=0.1
  - _openmp_mutex=4.5
  - _r-mutex=1.0.1
  - alsa-lib=1.2.7.2
  - amas=1.0
  - armadillo=10.8.2
  - arpack=3.7.0
  - attr=2.5.1
  - bcftools=1.17
  - bedtools=2.31.0
  - binutils_impl_linux-64=2.40
  - biopython=1.81
  - blast=2.13.0
  - boltons=23.0.0
  - boost-cpp=1.74.0
  - bowtie2=2.4.5
  - brotli=1.0.9
  - brotli-bin=1.0.9
  - bwa=0.7.17
  - bwidget=1.9.14
  - bzip2=1.0.8
  - c-ares=1.19.1
  - ca-certificates=2023.7.22
  - cairo=1.16.0
  - cd-hit=4.8.1
  - certifi=2023.7.22
  - cffi=1.15.1
  - charset-normalizer=3.1.0
  - circos=0.69.9
  - click=8.1.3
  - colorama=0.4.6
  - coloredlogs=15.0.1
  - colormath=3.0.0
  - conda=23.7.4
  - conda-package-handling=2.0.2
  - conda-package-streaming=0.8.0
  - contourpy=1.1.0
  - cryptography=39.0.0
  - csvtk=0.25.0
  - curl=7.88.1
  - cutadapt=4.4
  - cycler=0.11.0
  - dbus=1.13.6
  - diamond=2.1.4
  - dnaio=0.10.0
  - dos2unix=7.4.1
  - entrez-direct=16.2
  - ete3=3.1.3
  - exonerate=2.4.0
  - expat=2.5.0
  - fastqc=0.11.6
  - fasttree=2.1.11
  - fftw=3.3.10
  - fmt=9.1.0
  - font-ttf-dejavu-sans-mono=2.37
  - font-ttf-inconsolata=3.000
  - font-ttf-source-code-pro=2.038
  - font-ttf-ubuntu=0.83
  - fontconfig=2.14.2
  - fonts-conda-ecosystem=1
  - fonts-conda-forge=1
  - fonttools=4.40.0
  - freetype=2.12.1
  - fribidi=1.0.10
  - future=0.18.3
  - gcc_impl_linux-64=13.1.0
  - getorganelle=1.7.6.1
  - gettext=0.21.1
  - gfortran_impl_linux-64=13.1.0
  - giflib=5.2.1
  - glib=2.74.1
  - glib-tools=2.74.1
  - glimmerhmm=3.0.4
  - gmp=6.2.1
  - gmpy2=2.1.2
  - graphite2=1.3.13
  - gsl=2.7
  - gst-plugins-base=1.20.3
  - gstreamer=1.20.3
  - gxx_impl_linux-64=13.1.0
  - harfbuzz=5.3.0
  - htslib=1.17
  - humanfriendly=10.0
  - icu=70.1
  - idna=3.4
  - importlib-metadata=6.7.0
  - importlib-resources=5.12.0
  - importlib_resources=5.12.0
  - isa-l=2.30.0
  - jack=1.9.21
  - java-jdk=8.0.92
  - jinja2=3.1.2
  - joblib=1.2.0
  - jpeg=9e
  - jsonpatch=1.32
  - jsonpointer=2.0
  - k8=0.2.5
  - kernel-headers_linux-64=2.6.32
  - keyutils=1.6.1
  - kiwisolver=1.4.4
  - krb5=1.19.4
  - lame=3.100
  - lapack=3.9.0
  - lcms2=2.12
  - ld_impl_linux-64=2.40
  - lerc=4.0.0
  - libarchive=3.5.2
  - libblas=3.9.0
  - libbrotlicommon=1.0.9
  - libbrotlidec=1.0.9
  - libbrotlienc=1.0.9
  - libcap=2.66
  - libcblas=3.9.0
  - libclang=14.0.6
  - libclang13=14.0.6
  - libcups=2.3.3
  - libcurl=7.88.1
  - libdb=6.2.32
  - libdeflate=1.14
  - libedit=3.1.20221030
  - libev=4.33
  - libevent=2.1.10
  - libexpat=2.5.0
  - libffi=3.4.2
  - libflac=1.4.3
  - libgcc-devel_linux-64=13.1.0
  - libgcc-ng=13.1.0
  - libgd=2.3.3
  - libgfortran-ng=13.1.0
  - libgfortran5=13.1.0
  - libglib=2.74.1
  - libgomp=13.1.0
  - libiconv=1.17
  - libidn2=2.3.4
  - liblapack=3.9.0
  - libllvm14=14.0.6
  - libmamba=0.24.0
  - libmambapy=0.24.0
  - libnghttp2=1.51.0
  - libnsl=2.0.0
  - libogg=1.3.4
  - libopenblas=0.3.23
  - libopus=1.3.1
  - libpng=1.6.39
  - libpq=14.5
  - libsanitizer=13.1.0
  - libsndfile=1.1.0
  - libsolv=0.7.24
  - libsqlite=3.42.0
  - libssh2=1.10.0
  - libstdcxx-devel_linux-64=13.1.0
  - libstdcxx-ng=13.1.0
  - libtiff=4.4.0
  - libtool=2.4.7
  - libudev1=253
  - libunistring=0.9.10
  - libuuid=2.38.1
  - libvorbis=1.3.7
  - libwebp-base=1.3.0
  - libxcb=1.13
  - libxkbcommon=1.0.3
  - libxml2=2.9.14
  - libxslt=1.1.35
  - libzlib=1.2.13
  - lxml=4.9.1
  - lz4-c=1.9.4
  - lzo=2.10
  - lzstring=1.0.4
  - mafft=7.515
  - make=4.3
  - mamba=0.24.0
  - markdown=3.4.3
  - markdown-it-py=3.0.0
  - markov_clustering=0.0.6
  - markupsafe=2.1.3
  - matplotlib=3.8.0
  - matplotlib-base=3.8.0
  - mdurl=0.1.0
  - minimap2=2.26
  - mpc=1.3.1
  - mpfr=4.2.0
  - mpg123=1.31.3
  - mpmath=1.3.0
  - multiqc=1.14
  - munkres=1.1.4
  - mysql-common=8.0.32
  - mysql-libs=8.0.32
  - ncurses=6.4
  - networkx=3.1
  - newick_utils=1.6
  - nlopt=2.7.1
  - nspr=4.35
  - nss=3.92
  - numpy=1.24.2
  - openblas=0.3.23
  - openjdk=17.0.3
  - openjpeg=2.5.0
  - openssl=1.1.1w
  - packaging=23.1
  - pandas=2.0.3
  - pandoc=2.19.2
  - pango=1.50.12
  - pbzip2=1.1.13
  - pcre=8.45
  - pcre2=10.37
  - perl=5.32.1
  - perl-archive-tar=2.40
  - perl-b-cow=0.007
  - perl-carp=1.50
  - perl-clone=0.46
  - perl-common-sense=3.75
  - perl-compress-raw-bzip2=2.201
  - perl-compress-raw-zlib=2.202
  - perl-config-general=2.65
  - perl-digest-perl-md5=1.9
  - perl-encode=3.19
  - perl-exporter=5.74
  - perl-exporter-tiny=1.002002
  - perl-extutils-makemaker=7.70
  - perl-font-ttf=1.06
  - perl-gd=2.76
  - perl-inc-latest=0.500
  - perl-io-compress=2.201
  - perl-io-string=1.08
  - perl-io-zlib=1.14
  - perl-json=4.10
  - perl-json-xs=2.34
  - perl-list-moreutils=0.430
  - perl-list-moreutils-xs=0.430
  - perl-math-bezier=0.01
  - perl-math-round=0.07
  - perl-math-vecstat=0.08
  - perl-module-build=0.4234
  - perl-module-implementation=0.09
  - perl-module-runtime=0.016
  - perl-number-format=1.76
  - perl-params-validate=1.31
  - perl-parent=0.241
  - perl-pathtools=3.75
  - perl-readonly=2.05
  - perl-regexp-common=2017060201
  - perl-scalar-list-utils=1.63
  - perl-set-intspan=1.19
  - perl-statistics-basic=1.6611
  - perl-storable=3.15
  - perl-svg=2.87
  - perl-test-fatal=0.016
  - perl-text-format=0.62
  - perl-time-hires=1.9764
  - perl-try-tiny=0.31
  - perl-types-serialiser=1.01
  - perl-xml-parser=2.44_01
  - phyx=1.1
  - picard=3.1.0
  - pigz=2.6
  - pillow=9.2.0
  - pip=23.1.2
  - pixman=0.40.0
  - platformdirs=3.5.1
  - pluggy=1.0.0
  - ply=3.11
  - pooch=1.7.0
  - pthread-stubs=0.4
  - pulseaudio=14.0
  - pybind11-abi=4
  - pycosat=0.6.4
  - pycparser=2.21
  - pygments=2.15.1
  - pyopenssl=23.2.0
  - pyparsing=3.1.0
  - pyqt=5.15.7
  - pyqt5-sip=12.11.0
  - pysocks=1.7.1
  - python=3.9.15
  - python-dateutil=2.8.2
  - python-isal=1.1.0
  - python-tzdata=2023.3
  - python_abi=3.9
  - pytz=2023.3
  - pyyaml=6.0
  - qt-main=5.15.6
  - quast=5.2.0
  - r-base=4.0.5
  - readline=8.2
  - reproc=14.2.4
  - reproc-cpp=14.2.4
  - requests=2.31.0
  - rich=13.4.2
  - rich-click=1.6.1
  - ruamel.yaml=0.17.31
  - ruamel.yaml.clib=0.2.7
  - samtools=1.18
  - scikit-learn=1.3.1
  - scipy=1.10.1
  - sed=4.8
  - seqkit=2.3.1
  - setuptools=67.7.2
  - simplejson=3.19.1
  - sip=6.7.11
  - six=1.16.0
  - spades=3.13.0
  - spectra=0.0.11
  - sqlite=3.42.0
  - superlu=5.2.2
  - sympy=1.12
  - sysroot_linux-64=2.12
  - tbb=2020.2
  - threadpoolctl=3.2.0
  - tk=8.6.12
  - tktable=2.10
  - toml=0.10.2
  - tomli=2.0.1
  - toolz=0.12.0
  - tornado=6.3.3
  - tqdm=4.65.0
  - treeshrink=1.3.9
  - trim-galore=0.6.7
  - trimal=1.4.1
  - trimmomatic=0.39
  - typing-extensions=4.6.3
  - typing_extensions=4.6.3
  - tzdata=2023c
  - unicodedata2=15.0.0
  - urllib3=2.0.3
  - wget=1.20.3
  - wheel=0.40.0
  - wkhtmltopdf=0.12.4
  - xcb-util=0.4.0
  - xcb-util-image=0.4.0
  - xcb-util-keysyms=0.4.0
  - xcb-util-renderutil=0.3.9
  - xcb-util-wm=0.4.1
  - xopen=1.7.0
  - xorg-fixesproto=5.0
  - xorg-inputproto=2.3.2
  - xorg-kbproto=1.0.7
  - xorg-libice=1.0.10
  - xorg-libsm=1.2.3
  - xorg-libx11=1.8.4
  - xorg-libxau=1.0.11
  - xorg-libxdmcp=1.1.3
  - xorg-libxext=1.3.4
  - xorg-libxfixes=5.0.3
  - xorg-libxi=1.7.10
  - xorg-libxrender=0.9.10
  - xorg-libxt=1.3.0
  - xorg-libxtst=1.2.3
  - xorg-recordproto=1.14.2
  - xorg-renderproto=0.11.1
  - xorg-xextproto=7.3.0
  - xorg-xproto=7.0.31
  - xz=5.2.6
  - yaml=0.2.5
  - yaml-cpp=0.7.0
  - zipp=3.15.0
  - zlib=1.2.13
  - zstandard=0.19.0
  - zstd=1.5.2
  - pip:
      - psutil==5.9.5

Hopefully, all the package versions will be compatible throughout the pipeline!

Best regards, Bom

cpouchon commented 8 months ago

Hello Bom and Josh, I have specified now on the README to install it manually within your conda env. Conda should manage the different compatibilities. Cheers, Charles