Installation ABC Enhancer-Gene Detection

Bonjour

J'ai essayé d'installer sur un environnement conda l'outil ABC Enhancer Gene Dectection : Getting Started — ABC-Enhancer-Gene-Prediction documentation.
Dans le tuto, il passe par mamba mais je suis resté sur conda : conda env create -f workflow/envs/abcenv.yml
Cependant, cela n'a pas abouti a cause de conflits.
Y a t -il une alternative a son installation ?

Pour info voici le contenu de abcenv.yml :
name: abc-env
channels:

  • bioconda
  • conda-forge
  • defaults
  • anaconda
    dependencies:
  • _libgcc_mutex=0.1=conda_forge
  • _openmp_mutex=4.5=2_gnu
  • _r-mutex=1.0.1=anacondar_1
  • aioeasywebdav=2.4.0=pyha770c72_0
  • aiohttp=3.9.5=py310h2372a71_0
  • aiosignal=1.3.1=pyhd8ed1ab_0
  • alabaster=0.7.16=pyhd8ed1ab_0
  • alsa-lib=1.2.11=hd590300_1
  • amply=0.1.6=pyhd8ed1ab_0
  • appdirs=1.4.4=pyh9f0ad1d_0
  • async-timeout=4.0.3=pyhd8ed1ab_0
  • attmap=0.13.2=pyhd8ed1ab_0
  • attr=2.5.1=h166bdaf_1
  • attrs=23.2.0=pyh71513ae_0
  • aws-c-auth=0.7.22=h96bc93b_2
  • aws-c-cal=0.6.14=h88a6e22_1
  • aws-c-common=0.9.19=h4ab18f5_0
  • aws-c-compression=0.2.18=h83b837d_6
  • aws-c-event-stream=0.4.2=ha47c788_12
  • aws-c-http=0.8.1=h29d6fba_17
  • aws-c-io=0.14.8=h21d4f22_5
  • aws-c-mqtt=0.10.4=h759edc4_4
  • aws-c-s3=0.5.9=h594631b_3
  • aws-c-sdkutils=0.1.16=h83b837d_2
  • aws-checksums=0.1.18=h83b837d_6
  • aws-crt-cpp=0.26.9=he3a8b3b_0
  • aws-sdk-cpp=1.11.329=hba8bd5f_3
  • babel=2.14.0=pyhd8ed1ab_0
  • bcrypt=4.1.3=py310he421c4c_0
  • bedtools=2.26.0=0
  • binutils_impl_linux-64=2.40=ha1999f0_1
  • black=24.4.2=py310hff52083_0
  • boto3=1.34.114=pyhd8ed1ab_0
  • botocore=1.34.114=pyge310_1234567_0
  • brotli=1.1.0=hd590300_1
  • brotli-bin=1.1.0=hd590300_1
  • brotli-python=1.1.0=py310hc6cd4ac_1
  • bwidget=1.9.14=ha770c72_1
  • bzip2=1.0.8=hd590300_5
  • c-ares=1.28.1=hd590300_0
  • ca-certificates=2024.2.2=hbcca054_0
  • cachetools=5.3.3=pyhd8ed1ab_0
  • cairo=1.18.0=h3faef2a_0
  • certifi=2024.2.2=pyhd8ed1ab_0
  • cffi=1.16.0=py310h2fee648_0
  • charset-normalizer=3.3.2=pyhd8ed1ab_0
  • click=8.1.7=unix_pyh707e725_0
  • coin-or-cbc=2.10.10=h9002f0b_0
  • coin-or-cgl=0.60.7=h516709c_0
  • coin-or-clp=1.17.8=h1ee7a9c_0
  • coin-or-osi=0.108.10=haf5fa05_0
  • coin-or-utils=2.11.11=hee58242_0
  • coincbc=2.10.10=0_metapackage
  • colorama=0.4.6=pyhd8ed1ab_0
  • configargparse=1.7=pyhd8ed1ab_0
  • connection_pool=0.0.3=pyhd3deb0d_0
  • contourpy=1.2.1=py310hd41b1e2_0
  • cryptography=42.0.7=py310hb1bd9d3_0
  • curl=8.8.0=he654da7_0
  • cycler=0.12.1=pyhd8ed1ab_0
  • datrie=0.8.2=py310h2372a71_7
  • dbus=1.13.6=h5008d03_3
  • defusedxml=0.7.1=pyhd8ed1ab_0
  • dpath=2.1.6=pyha770c72_0
  • dropbox=11.36.2=pyhd8ed1ab_0
  • eido=0.2.2=pyhd8ed1ab_0
  • exceptiongroup=1.2.0=pyhd8ed1ab_2
  • execnet=2.1.1=pyhd8ed1ab_0
  • expat=2.6.2=h59595ed_0
  • filechunkio=1.8=py_2
  • 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=h77eed37_2
  • fontconfig=2.14.2=h14ed4e7_0
  • fonts-conda-ecosystem=1=0
  • fonts-conda-forge=1=0
  • fonttools=4.52.4=py310hc51659f_0
  • freetype=2.12.1=h267a509_2
  • fribidi=1.0.10=h36c2ea0_0
  • frozenlist=1.4.1=py310h2372a71_0
  • ftputil=5.1.0=pyhd8ed1ab_0
  • gcc=13.2.0=hc7bed06_7
  • gcc_impl_linux-64=13.2.0=h9eb54c0_7
  • gettext=0.22.5=h59595ed_2
  • gettext-tools=0.22.5=h59595ed_2
  • gflags=2.2.2=he1b5a44_1004
  • gfortran_impl_linux-64=13.2.0=h738fc78_7
  • gitdb=4.0.11=pyhd8ed1ab_0
  • gitpython=3.1.43=pyhd8ed1ab_0
  • glib=2.80.2=hf974151_0
  • glib-tools=2.80.2=hb6ce0ca_0
  • glog=0.7.0=hed5481d_0
  • google-api-core=2.19.0=pyhd8ed1ab_0
  • google-api-python-client=2.131.0=pyhd8ed1ab_0
  • google-auth=2.29.0=pyhca7485f_0
  • google-auth-httplib2=0.2.0=pyhd8ed1ab_0
  • google-cloud-core=2.4.1=pyhd8ed1ab_0
  • google-cloud-storage=2.16.0=pyhca7485f_0
  • google-crc32c=1.1.2=py310hc5c09a0_5
  • google-resumable-media=2.7.0=pyhd8ed1ab_0
  • googleapis-common-protos=1.63.0=pyhd8ed1ab_0
  • graphite2=1.3.13=h59595ed_1003
  • grpcio=1.62.2=py310h1b8f574_0
  • gst-plugins-base=1.24.4=h9ad1361_0
  • gstreamer=1.24.4=haf2f30d_0
  • gxx=13.2.0=hc7bed06_7
  • gxx_impl_linux-64=13.2.0=h2a599c4_7
  • harfbuzz=8.5.0=hfac3d4d_0
  • htslib=1.20=h81da01d_0
  • httplib2=0.22.0=pyhd8ed1ab_0
  • humanfriendly=10.0=pyhd8ed1ab_6
  • icu=73.2=h59595ed_0
  • idna=3.7=pyhd8ed1ab_0
  • imagesize=1.4.1=pyhd8ed1ab_0
  • importlib-metadata=7.1.0=pyha770c72_0
  • importlib_resources=6.4.0=pyhd8ed1ab_0
  • iniconfig=2.0.0=pyhd8ed1ab_0
  • jinja2=3.1.4=pyhd8ed1ab_0
  • jmespath=1.0.1=pyhd8ed1ab_0
  • jsonschema=4.22.0=pyhd8ed1ab_0
  • jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
  • jupyter_core=5.7.2=py310hff52083_0
  • kernel-headers_linux-64=2.6.32=he073ed8_17
  • keyutils=1.6.1=h166bdaf_0
  • kiwisolver=1.4.5=py310hd41b1e2_1
  • krb5=1.21.2=h659d440_0
  • lame=3.100=h166bdaf_1003
  • lcms2=2.16=hb7c19ff_0
  • ld_impl_linux-64=2.40=hf3520f5_1
  • lerc=4.0.0=h27087fc_0
  • libabseil=20240116.2=cxx17_h59595ed_0
  • libarrow=16.1.0=hcb6531f_6_cpu
  • libarrow-acero=16.1.0=hac33072_6_cpu
  • libarrow-dataset=16.1.0=hac33072_6_cpu
  • libarrow-substrait=16.1.0=h7e0c224_6_cpu
  • libasprintf=0.22.5=h661eb56_2
  • libasprintf-devel=0.22.5=h661eb56_2
  • libblas=3.9.0=22_linux64_openblas
  • libbrotlicommon=1.1.0=hd590300_1
  • libbrotlidec=1.1.0=hd590300_1
  • libbrotlienc=1.1.0=hd590300_1
  • libcap=2.69=h0f662aa_0
  • libcblas=3.9.0=22_linux64_openblas
  • libclang-cpp15=15.0.7=default_h127d8a8_5
  • libclang13=18.1.6=default_h5d6823c_0
  • libcrc32c=1.1.2=h9c3ff4c_0
  • libcups=2.3.3=h4637d8d_4
  • libcurl=8.8.0=hca28451_0
  • libdeflate=1.20=hd590300_0
  • libedit=3.1.20191231=he28a2e2_2
  • libev=4.33=hd590300_2
  • libevent=2.1.12=hf998b51_1
  • libexpat=2.6.2=h59595ed_0
  • libffi=3.4.2=h7f98852_5
  • libflac=1.4.3=h59595ed_0
  • libgcc=7.2.0=h69d50b8_2
  • libgcc-devel_linux-64=13.2.0=hceb6213_107
  • libgcc-ng=13.2.0=h77fa898_7
  • libgcrypt=1.10.3=hd590300_0
  • libgettextpo=0.22.5=h59595ed_2
  • libgettextpo-devel=0.22.5=h59595ed_2
  • libgfortran-ng=13.2.0=h69a702a_7
  • libgfortran5=13.2.0=hca663fb_7
  • libglib=2.80.2=hf974151_0
  • libgomp=13.2.0=h77fa898_7
  • libgoogle-cloud=2.24.0=h2736e30_0
  • libgoogle-cloud-storage=2.24.0=h3d9a0c8_0
  • libgpg-error=1.49=h4f305b6_0
  • libgrpc=1.62.2=h15f2491_0
  • libiconv=1.17=hd590300_2
  • libjpeg-turbo=3.0.0=hd590300_1
  • liblapack=3.9.0=22_linux64_openblas
  • liblapacke=3.9.0=22_linux64_openblas
  • libllvm15=15.0.7=hb3ce162_4
  • libllvm18=18.1.6=hb77312f_0
  • libnghttp2=1.58.0=h47da74e_1
  • libnsl=2.0.1=hd590300_0
  • libogg=1.3.4=h7f98852_1
  • libopenblas=0.3.27=pthreads_h413a1c8_0
  • libopus=1.3.1=h7f98852_1
  • libparquet=16.1.0=h6a7eafb_6_cpu
  • libpng=1.6.43=h2797004_0
  • libpq=16.3=ha72fbe1_0
  • libprotobuf=4.25.3=h08a7969_0
  • libre2-11=2023.09.01=h5a48ba9_2
  • libsanitizer=13.2.0=h6ddb7a1_7
  • libsndfile=1.2.2=hc60ed4a_1
  • libsodium=1.0.18=h36c2ea0_1
  • libsqlite=3.45.3=h2797004_0
  • libssh2=1.11.0=h0841786_0
  • libstdcxx-devel_linux-64=13.2.0=hceb6213_107
  • libstdcxx-ng=13.2.0=hc0a3c3a_7
  • libsystemd0=255=h3516f8a_1
  • libthrift=0.19.0=hb90f79a_1
  • libtiff=4.6.0=h1dd3fc0_3
  • libutf8proc=2.8.0=h166bdaf_0
  • libuuid=2.38.1=h0b41bf4_0
  • libvorbis=1.3.7=h9c3ff4c_0
  • libwebp-base=1.4.0=hd590300_0
  • libxcb=1.15=h0b41bf4_0
  • libxcrypt=4.4.36=hd590300_1
  • libxkbcommon=1.7.0=h662e7e4_0
  • libxml2=2.12.7=hc051c1a_0
  • libzlib=1.2.13=h4ab18f5_6
  • logmuse=0.2.6=pyh8c360ce_0
  • lz4-c=1.9.4=hcb278e6_0
  • macs2=2.2.9.1=py310h4b81fae_0
  • make=4.3=hd18ef5c_1
  • markdown-it-py=3.0.0=pyhd8ed1ab_0
  • markupsafe=2.1.5=py310h2372a71_0
  • matplotlib=3.8.4=py310hff52083_2
  • matplotlib-base=3.8.4=py310hef631a5_2
  • mdurl=0.1.2=pyhd8ed1ab_0
  • mpg123=1.32.6=h59595ed_0
  • multidict=6.0.5=py310h2372a71_0
  • munkres=1.0.7=py_1
  • mypy_extensions=1.0.0=pyha770c72_0
  • mysql-common=8.3.0=hf1915f5_4
  • mysql-libs=8.3.0=hca2cd23_4
  • natsort=8.4.0=pyhd8ed1ab_0
  • nbformat=5.10.4=pyhd8ed1ab_0
  • ncls=0.0.68=py310h4b81fae_2
  • ncurses=6.5=h59595ed_0
  • nspr=4.35=h27087fc_0
  • nss=3.100=hca3bf56_0
  • numpy=1.26.4=py310hb13e2d6_0
  • oauth2client=4.1.3=py_0
  • openjpeg=2.5.2=h488ebb8_0
  • openssl=3.3.0=h4ab18f5_3
  • orc=2.0.1=h17fec99_1
  • packaging=24.0=pyhd8ed1ab_0
  • pandas=2.2.2=py310hf9f9076_1
  • pango=1.52.2=ha41ecd1_0
  • paramiko=3.4.0=pyhd8ed1ab_0
  • pathspec=0.12.1=pyhd8ed1ab_0
  • patsy=0.5.6=pyhd8ed1ab_0
  • pcre2=10.43=hcad00b1_0
  • peppy=0.40.2=pyhd8ed1ab_0
  • pillow=10.3.0=py310hf73ecf8_0
  • pip=24.0=pyhd8ed1ab_0
  • pixman=0.43.2=h59595ed_0
  • pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
  • plac=1.4.3=pyhd8ed1ab_0
  • platformdirs=4.2.2=pyhd8ed1ab_0
  • pluggy=1.5.0=pyhd8ed1ab_0
  • ply=3.11=pyhd8ed1ab_2
  • prettytable=3.10.0=pyhd8ed1ab_0
  • proto-plus=1.23.0=pyhd8ed1ab_0
  • protobuf=4.25.3=py310ha8c1f0e_0
  • psutil=5.9.8=py310h2372a71_0
  • pthread-stubs=0.4=h36c2ea0_1001
  • pulp=2.7.0=py310hff52083_1
  • pulseaudio-client=17.0=hb77b528_0
  • pyarrow=16.1.0=py310h17c5347_1
  • pyarrow-core=16.1.0=py310h6f79a3a_1_cpu
  • pyasn1=0.6.0=pyhd8ed1ab_0
  • pyasn1-modules=0.4.0=pyhd8ed1ab_0
  • pybigwig=0.3.22=py310h79000e5_2
  • pycparser=2.22=pyhd8ed1ab_0
  • pygments=2.18.0=pyhd8ed1ab_0
  • pynacl=1.5.0=py310h2372a71_3
  • pyopenssl=24.0.0=pyhd8ed1ab_0
  • pyparsing=3.1.2=pyhd8ed1ab_0
  • pyqt=5.15.9=py310h04931ad_5
  • pyqt5-sip=12.12.2=py310hc6cd4ac_5
  • pyranges=0.0.129=pyh7cba7a3_0
  • pyrle=0.0.40=py310h4b81fae_0
  • pysam=0.22.1=py310h41dec4a_0
  • pysftp=0.2.9=py_1
  • pysocks=1.7.1=pyha2e5f31_6
  • pytest=8.2.1=pyhd8ed1ab_0
  • pytest-xdist=3.5.0=pyhd8ed1ab_0
  • python=3.10.14=hd12c33a_0_cpython
  • python-dateutil=2.9.0=pyhd8ed1ab_0
  • python-fastjsonschema=2.19.1=pyhd8ed1ab_0
  • python-irodsclient=2.0.1=pyhd8ed1ab_0
  • python-tzdata=2024.1=pyhd8ed1ab_0
  • python_abi=3.10=4_cp310
  • pytz=2024.1=pyhd8ed1ab_0
  • pyu2f=0.1.5=pyhd8ed1ab_0
  • pyyaml=6.0.1=py310h2372a71_1
  • qt-main=5.15.8=hc9dc06e_21
  • r-base=4.3.3=hf0d99cb_1
  • re2=2023.09.01=h7f4b329_2
  • readline=8.2=h8228510_1
  • referencing=0.35.1=pyhd8ed1ab_0
  • requests=2.32.2=pyhd8ed1ab_0
  • reretry=0.11.8=pyhd8ed1ab_0
  • rich=13.7.1=pyhd8ed1ab_0
  • rpds-py=0.18.1=py310he421c4c_0
  • rsa=4.9=pyhd8ed1ab_0
  • s2n=1.4.15=he19d79f_0
  • s3transfer=0.10.1=pyhd8ed1ab_0
  • samtools=1.20=h50ea8bc_0
  • scipy=1.13.1=py310h93e2701_0
  • seaborn=0.13.2=hd8ed1ab_2
  • seaborn-base=0.13.2=pyhd8ed1ab_2
  • sed=4.8=he412f7d_0
  • setuptools=70.0.0=pyhd8ed1ab_0
  • setuptools-scm=8.1.0=pyhd8ed1ab_0
  • sip=6.7.12=py310hc6cd4ac_0
  • six=1.16.0=pyh6c4a22f_0
  • slacker=0.14.0=py_0
  • smart_open=6.4.0=pyhd8ed1ab_0
  • smmap=5.0.0=pyhd8ed1ab_0
  • snakemake=7.32.4=hdfd78af_1
  • snakemake-minimal=7.32.4=pyhdfd78af_1
  • snappy=1.2.0=hdb0a2a9_1
  • snowballstemmer=2.2.0=pyhd8ed1ab_0
  • sorted_nearest=0.0.39=py310h4b81fae_1
  • sphinx=7.3.7=pyhd8ed1ab_0
  • sphinxcontrib-applehelp=1.0.8=pyhd8ed1ab_0
  • sphinxcontrib-devhelp=1.0.6=pyhd8ed1ab_0
  • sphinxcontrib-htmlhelp=2.0.5=pyhd8ed1ab_0
  • sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
  • sphinxcontrib-qthelp=1.0.7=pyhd8ed1ab_0
  • sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_0
  • statsmodels=0.14.2=py310h261611a_0
  • stone=3.3.6=pyhd8ed1ab_0
  • stopit=1.1.2=py_0
  • sysroot_linux-64=2.12=he073ed8_17
  • tabix=1.11=hdfd78af_0
  • tabulate=0.9.0=pyhd8ed1ab_1
  • throttler=1.2.2=pyhd8ed1ab_0
  • tk=8.6.13=noxft_h4845f30_101
  • tktable=2.10=h0c5db8f_5
  • toml=0.10.2=pyhd8ed1ab_0
  • tomli=2.0.1=pyhd8ed1ab_0
  • toposort=1.10=pyhd8ed1ab_0
  • tornado=6.4=py310h2372a71_0
  • traitlets=5.14.3=pyhd8ed1ab_0
  • typing-extensions=4.11.0=hd8ed1ab_0
  • typing_extensions=4.11.0=pyha770c72_0
  • tzdata=2024a=h0c530f3_0
  • ubiquerg=0.7.0=pyhd8ed1ab_0
  • unicodedata2=15.1.0=py310h2372a71_0
  • uritemplate=4.1.1=pyhd8ed1ab_0
  • urllib3=2.2.1=pyhd8ed1ab_0
  • veracitools=0.1.3=py_0
  • wcwidth=0.2.13=pyhd8ed1ab_0
  • wheel=0.43.0=pyhd8ed1ab_1
  • wrapt=1.16.0=py310h2372a71_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=2.41=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=1.8.9=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
  • yaml=0.2.5=h7f98852_2
  • yarl=1.9.4=py310h2372a71_0
  • yte=1.5.4=pyha770c72_0
  • zipp=3.17.0=pyhd8ed1ab_0
  • zlib=1.2.13=h4ab18f5_6
  • zstd=1.5.6=ha6fb4c9_0
  • hic-straw==1.3.1
  • pip:
    • docutils==0.20.1
    • pybind11==2.12.0
    • sphinx-rtd-theme==2.0.0
    • sphinxcontrib-jquery==4.1

Merci d'avanve pour votre aide

Thibaut

Bonjour,

Essayer avec mamba. La résolution est différente et peut aboutir.

Bonjour

Merci pour le conseil, effectivement, c'était plus rapide.
En revanche, plusieurs problèmes persistent :

Encountered problems while solving:

  • package botocore-1.34.114-pyge310_1234567_0 is excluded by strict repo priority
  • package c-ares-1.28.1-hd590300_0 is excluded by strict repo priority
  • package filechunkio-1.8-py_2 is excluded by strict repo priority
  • package ftputil-5.1.0-pyhd8ed1ab_0 is excluded by strict repo priority
  • package google-api-python-client-2.131.0-pyhd8ed1ab_0 is excluded by strict repo priority
  • package libdeflate-1.20-hd590300_0 is excluded by strict repo priority
  • package oauth2client-4.1.3-py_0 is excluded by strict repo priority
  • package pyasn1-modules-0.4.0-pyhd8ed1ab_0 is excluded by strict repo priority
  • package rsa-4.9-pyhd8ed1ab_0 is excluded by strict repo priority
  • package uritemplate-4.1.1-pyhd8ed1ab_0 is excluded by strict repo priority
  • package urllib3-2.2.1-pyhd8ed1ab_0 is excluded by strict repo priority
  • package dropbox-11.36.2-pyhd8ed1ab_0 is excluded by strict repo priority
  • package pynacl-1.5.0-py310h2372a71_3 is excluded by strict repo priority
  • package toposort-1.10-pyhd8ed1ab_0 is excluded by strict repo priority
  • package pysftp-0.2.9-py_1 is excluded by strict repo priority

J'ai solutionné le problème en changeant la config de conda
conda config --set channel_priority flexible

Bonjour

Après plusieurs jours d'échec a utiliser abc-env après avoir installé son environnement conda, je voulais savoir s'il était possible de l'installer. En effet, je rencontre des problèmes de version de python entre celle de l'environnement et celle de jupyter lab lorsque je lance l'outil.
Pouvez-vous l'installer s'il vous plait ?: GitHub - broadinstitute/ABC-Enhancer-Gene-Prediction: Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
Documentation : Getting Started — ABC-Enhancer-Gene-Prediction documentation

En vous remerciant par avance pour votre aide !

Thibaut