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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 9 months ago

jmhallas commented 1 year 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 1 year 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 1 year 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 1 year 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