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VGP / vgp-assembly

VGP repository for the genome assembly working group
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Problem install conda environment #81

Closed gubrins closed 1 year ago

gubrins commented 1 year ago

Heys,

So I am trying to set up a new environment: conda env create -f mitoVGP_conda_env_pacbio.yml

And I am getting this error:

ResolvePackageNotFound: - r-base==3.2.2=0

Did anybody has a similar issue? Thanks in advance!

gf777 commented 1 year ago

Seems like that version of r-base is not available anymore. I tried removing the specification and it installed correctly. Can you try the same? You can use the new yaml https://github.com/gf777/mitoVGP/blob/master/mitoVGP_conda_env_pacbio.yml

Let me know. Thanks

Giulio

gubrins commented 1 year ago

Thanks Giulio for your fast reply. It did not work, a lot of conflicts were raised, here some examples:

Package biopython conflicts for:
genomicconsensus==2.3.3=py27_0 -> pbcore[version='>=1.6.5'] -> biopython[version='>=1.74']
pbcoretools==0.2.4=py27_4 -> pbcore[version='>=1.6.5'] -> biopython[version='>=1.74']

Package glib-tools conflicts for:
r-base -> glib[version='>=2.69.1,<3.0a0'] -> glib-tools[version='2.66.4|2.66.4|2.66.4|2.66.4|2.66.5|2.66.5|2.66.5|2.66.5|2.66.6|2.66.6|2.66.6|2.66.6|2.66.6|2.66.7|2.66.7|2.68.0|2.68.0|2.68.1|2.68.2|2.68.2|2.68.2|2.68.3|2.68.4|2.68.4|2.70.0|2.70.0|2.70.1|2.70.2|2.70.2|2.70.2|2.70.2|2.70.2|2.72.1',build='h709712a_2|hc4f0c31_2|h709712a_2|hc4f0c31_2|ha03b18c_2|hcd2ae1e_2|hc4f0c31_2|h9c3ff4c_0|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h780b84a_1|h780b84a_2|h780b84a_4|h6239696_0|h780b84a_3|h780b84a_1|h780b84a_0|h780b84a_0|h780b84a_0|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_3|ha03b18c_2|h709712a_2|hcd2ae1e_2|hcd2ae1e_2|ha03b18c_2']
cairo==1.16.0=hfb77d84_1002 -> glib[version='>=2.58.3,<3.0a0'] -> glib-tools[version='2.66.4|2.66.4|2.66.4|2.66.4|2.66.5|2.66.5|2.66.5|2.66.5|2.66.6|2.66.6|2.66.6|2.66.6|2.66.6|2.66.7|2.66.7|2.68.0|2.68.0|2.68.1|2.68.2|2.68.2|2.68.2|2.68.3|2.68.4|2.68.4|2.70.0|2.70.0|2.70.1|2.70.2|2.70.2|2.70.2|2.70.2|2.70.2|2.72.1',build='h709712a_2|hc4f0c31_2|h709712a_2|hc4f0c31_2|ha03b18c_2|hcd2ae1e_2|hc4f0c31_2|h9c3ff4c_0|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h780b84a_1|h780b84a_2|h780b84a_4|h6239696_0|h780b84a_3|h780b84a_1|h780b84a_0|h780b84a_0|h780b84a_0|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_3|ha03b18c_2|h709712a_2|hcd2ae1e_2|hcd2ae1e_2|ha03b18c_2']
harfbuzz==2.4.0=h9f30f68_3 -> glib[version='>=2.58.3,<3.0a0'] -> glib-tools[version='2.66.4|2.66.4|2.66.4|2.66.4|2.66.5|2.66.5|2.66.5|2.66.5|2.66.6|2.66.6|2.66.6|2.66.6|2.66.6|2.66.7|2.66.7|2.68.0|2.68.0|2.68.1|2.68.2|2.68.2|2.68.2|2.68.3|2.68.4|2.68.4|2.70.0|2.70.0|2.70.1|2.70.2|2.70.2|2.70.2|2.70.2|2.70.2|2.72.1',build='h709712a_2|hc4f0c31_2|h709712a_2|hc4f0c31_2|ha03b18c_2|hcd2ae1e_2|hc4f0c31_2|h9c3ff4c_0|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h9c3ff4c_1|h780b84a_1|h780b84a_2|h780b84a_4|h6239696_0|h780b84a_3|h780b84a_1|h780b84a_0|h780b84a_0|h780b84a_0|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_0|h9c3ff4c_0|h9c3ff4c_2|h9c3ff4c_3|ha03b18c_2|h709712a_2|hcd2ae1e_2|hcd2ae1e_2|ha03b18c_2']

Package xorg-libxrender conflicts for:
r-base -> xorg-libxrender
openjdk==11.0.1=h46a85a0_1017 -> xorg-libxrender
pango==1.42.4=ha030887_1 -> cairo[version='>=1.16.0,<1.17.0a0'] -> xorg-libxrender
cairo==1.16.0=hfb77d84_1002 -> xorg-libxrender
picard==2.20.6=0 -> openjdk[version='>=8'] -> xorg-libxrender
harfbuzz==2.4.0=h9f30f68_3 -> cairo[version='>=1.16.0,<1.17.0a0'] -> xorg-libxrender
xorg-libxrender==0.9.10=h516909a_1002

Package boost conflicts for:
boost==1.70.0=py27h9de70de_1
blast==2.5.0=hc0b0e79_3 -> boost

Package python-consensuscore conflicts for:
genomicconsensus==2.3.3=py27_0 -> python-consensuscore[version='>=1.1.1']
python-consensuscore==1.1.1=py27h3f2a3d2_3

Package python-consensuscore2 conflicts for:
python-consensuscore2==3.4.1=py27_0
genomicconsensus==2.3.3=py27_0 -> python-consensuscore2[version='>=3.4.1']The following specifications were found to be incompatible with your system:

- feature:/linux-64::__glibc==2.31=0
  - feature:/linux-64::__unix==0=0
  - feature:|@/linux-64::__unix==0=0
  - alsa-lib==1.1.5=h516909a_1001 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - bcftools==1.9=ha228f0b_4 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
  - blast==2.5.0=hc0b0e79_3 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']

and at the end I have this:

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.

But no new environment is created.

gf777 commented 1 year ago

Ah I see what the problem likely is. You have your conda config file overriding channel priority. You need to edit your .condarc. file (usually in the home directory) setting priority to flexible:

auto_activate_base: true
anaconda_upload: false
channels:
  - conda-forge
  - bioconda
  - r
  - bioconda/label/cf201901
  - biobuilds
  - yuxiang
  - defaults
channel_priority: flexible

I just tested the installation again, and it works fine in my conda (version 4.13.0). See log below. Hope this helps!


(base) [gformenti@login04 gformenti]$ conda remove --name mitoVGP_pacbio --all

Remove all packages in environment ...:

## Package Plan ##

  environment location: ...

The following packages will be REMOVED:

  _libgcc_mutex-0.1-main
  _r-mutex-1.0.1-anacondar_1
  alsa-lib-1.1.5-h516909a_1001
  avro-python2-1.9.0-py_0
  awscli-1.16.225-py27_0
  bam2fastq-1.1.0-0
  bcftools-1.9-ha228f0b_4
  blast-2.5.0-hc0b0e79_3
  boost-1.70.0-py27h9de70de_1
  boost-cpp-1.70.0-h8e57a91_2
  botocore-1.12.215-py_0
  bowtie2-2.3.4.1-py27h2d50403_1
  bzip2-1.0.8-h516909a_2
  ca-certificates-2019.11.28-hecc5488_0
  cairo-1.16.0-hfb77d84_1002
  certifi-2019.11.28-py27_0
  cffi-1.13.2-py27h8022711_0
  chardet-3.0.4-py27_1003
  colorama-0.3.9-py27_0
  cryptography-2.8-py27h72c5cf5_1
  curl-7.65.3-hf8cf82a_0
  cython-0.29.14-py27he1b5a44_0
  docutils-0.15.2-py27_0
  enum34-1.1.6-py27_1002
  fontconfig-2.13.1-h86ecdb6_1001
  freebayes-1.0.2-0
  freetype-2.10.0-he983fc9_1
  fribidi-1.0.5-h516909a_1002
  futures-3.3.0-py27_0
  genomicconsensus-2.3.3-py27_0
  gettext-0.19.8.1-hc5be6a0_1002
  giflib-5.1.7-h516909a_1
  glib-2.58.3-py27h6f030ca_1002
  graphite2-1.3.13-hf484d3e_1000
  h5py-2.10.0-nompi_py27h513d04c_100
  harfbuzz-2.4.0-h9f30f68_3
  hdf5-1.10.5-nompi_h3c11f04_1104
  htslib-1.9-ha228f0b_7
  icu-64.2-he1b5a44_1
  idna-2.8-py27_1000
  infernal-1.1.2-h14c3975_2
  ipaddress-1.0.23-py_0
  iso8601-0.1.12-py_1
  java-jdk-7.0.91-1
  jmespath-0.9.4-py_0
  jpeg-9c-h14c3975_1001
  krb5-1.16.3-h05b26f9_1001
  lcms2-2.9-hbd6801e_1
  libblas-3.8.0-14_openblas
  libcblas-3.8.0-14_openblas
  libcurl-7.65.3-hda55be3_0
  libdeflate-1.0-h14c3975_1
  libedit-3.1.20170329-hf8c457e_1001
  libffi-3.2.1-he1b5a44_1006
  libgcc-7.2.0-h69d50b8_2
  libgcc-ng-9.2.0-hdf63c60_0
  libgfortran-ng-7.3.0-hdf63c60_2
  libiconv-1.15-h516909a_1005
  liblapack-3.8.0-14_openblas
  libopenblas-0.3.7-h5ec1e0e_5
  libpng-1.6.37-hed695b0_0
  libssh2-1.8.2-h22169c7_2
  libstdcxx-ng-9.2.0-hdf63c60_0
  libtiff-4.1.0-hc3755c2_1
  libuuid-2.32.1-h14c3975_1000
  libxcb-1.13-h14c3975_1002
  libxml2-2.9.10-hee79883_0
  linecache2-1.0.0-py_1
  lz4-c-1.8.3-he1b5a44_1001
  minimap2-2.17-h8b12597_1
  mummer-3.23-pl526_8
  muscle-3.8.1551-h6bb024c_4
  ncurses-6.1-hf484d3e_1002
  numpy-1.16.5-py27h95a1406_0
  openjdk-11.0.1-h46a85a0_1017
  openssl-1.1.1d-h516909a_0
  pango-1.42.4-ha030887_1
  pbbam-0.23.0-h88345a9_0
  pbcommand-1.1.1-py_3
  pbcopper-0.4.2-h3f2a3d2_1
  pbcore-1.7.1-py27_0
  pbcoretools-0.2.4-py27_4
  pbgcpp-1.9.0-0
  pbmm2-1.0.0-ha888412_0
  pcre-8.43-he1b5a44_0
  perl-5.26.2-h516909a_1006
  picard-2.20.6-0
  pip-19.3.1-py27_0
  pixman-0.38.0-h516909a_1003
  pthread-stubs-0.4-h14c3975_1001
  pyasn1-0.4.8-py_0
  pycparser-2.19-py27_1
  pyopenssl-19.1.0-py27_0
  pysam-0.15.3-py27hda2845c_1
  pysocks-1.7.1-py27_0
  python-2.7.15-h5a48372_1009
  python-consensuscore-1.1.1-py27h3f2a3d2_3
  python-consensuscore2-3.4.1-py27_0
  python-dateutil-2.8.1-py_0
  pytz-2019.3-py_0
  pyyaml-5.2-py27h516909a_0
  r-base-3.2.2-1
  readline-8.0-hf8c457e_0
  requests-2.22.0-py27_1
  rsa-3.4.2-py_1
  s3transfer-0.2.1-py27_0
  samtools-1.9-h8571acd_11
  setuptools-42.0.2-py27_0
  six-1.13.0-py27_0
  sqlite-3.30.1-hcee41ef_0
  tbb-2019.9-hc9558a2_1
  tk-8.6.10-hed695b0_0
  traceback2-1.4.0-py27_0
  trnascan-se-2.0-pl526h470a237_1
  unittest2-1.1.0-py_0
  urllib3-1.25.7-py27_0
  wheel-0.33.6-py27_0
  xorg-fixesproto-5.0-h14c3975_1002
  xorg-inputproto-2.3.2-h14c3975_1002
  xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice-1.0.10-h516909a_0
  xorg-libsm-1.2.3-h84519dc_1000
  xorg-libx11-1.6.9-h516909a_0
  xorg-libxau-1.0.9-h14c3975_0
  xorg-libxdmcp-1.1.3-h516909a_0
  xorg-libxext-1.3.4-h516909a_0
  xorg-libxfixes-5.0.3-h516909a_1004
  xorg-libxi-1.7.10-h516909a_0
  xorg-libxrender-0.9.10-h516909a_1002
  xorg-libxtst-1.2.3-h516909a_1002
  xorg-recordproto-1.14.2-h516909a_1002
  xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto-7.0.31-h14c3975_1007
  xz-5.2.4-h14c3975_1001
  yaml-0.2.2-h516909a_1
  zlib-1.2.11-h516909a_1006
  zstd-1.4.4-h3b9ef0a_1

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(base) [gformenti@login04 gformenti]$ wget https://raw.githubusercontent.com/gf777/mitoVGP/master/mitoVGP_conda_env_pacbio.yml
--2022-09-16 08:47:30--  https://raw.githubusercontent.com/gf777/mitoVGP/master/mitoVGP_conda_env_pacbio.yml
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 4273 (4.2K) [text/plain]
Saving to: ‘mitoVGP_conda_env_pacbio.yml’

100%[=====================================================================================================>] 4,273       --.-K/s   in 0.002s  

2022-09-16 08:47:30 (2.55 MB/s) - ‘mitoVGP_conda_env_pacbio.yml’ saved [4273/4273]

(base) [gformenti@login04 gformenti]$ conda env create -f mitoVGP_conda_env_pacbio.yml
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.13.0
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base conda

Preparing transaction: done
Verifying transaction: done
Executing transaction: \
gubrins commented 1 year ago

amazing! Thanks Giulio!!