conda is not installing the new version of bcftools (1.14)

[Elif Özçelik (Student)]

Hi, I am specifying the label as "main" mentioned in https://anaconda.org/bioconda/bcftools but still, conda install -c bioconda/label/main bcftools this command installs me the bcftools version 1.9, as can be seen below:

The following NEW packages will be INSTALLED:

  bcftools           bioconda/label/main/linux-64::bcftools-1.9-ha228f0b_4

How do I fix this problem, thanks. 

[Ariel Balter]

Conda always installs the latest by default. If you want a specific version, you can use the `<package>=<version>` syntax.

v1.14 is the latest:

So that is what conda will install by default.

```

(base) balter@winmac:~$ conda create -n bcftools -c bioconda bcftools -y
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/balter/conda/envs/bcftools

  added / updated specs:
    - bcftools

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  bcftools           bioconda/linux-64::bcftools-1.14-h88f3f91_0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
  gsl                conda-forge/linux-64::gsl-2.6-he838d99_2
  htslib             bioconda/linux-64::htslib-1.14-h9093b5e_0
  krb5               conda-forge/linux-64::krb5-1.19.2-hcc1bbae_3
  libblas            conda-forge/linux-64::libblas-3.9.0-12_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-12_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-7.80.0-h2574ce0_0
  libdeflate         conda-forge/linux-64::libdeflate-1.7-h7f98852_5
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libgcc-ng          conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_11
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_11
  libgfortran5       conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_11
  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_11
  libnghttp2         conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_1
  libopenblas        conda-forge/linux-64::libopenblas-0.3.18-pthreads_h8fe5266_0
  libssh2            conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_11
  libzlib            conda-forge/linux-64::libzlib-1.2.11-h36c2ea0_1013
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  openssl            conda-forge/linux-64::openssl-1.1.1l-h7f98852_0
  perl               conda-forge/linux-64::perl-5.32.1-1_h7f98852_perl5
  tk                 conda-forge/linux-64::tk-8.6.11-h27826a3_1
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h36c2ea0_1013


Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate bcftools
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) balter@winmac:~$

```

[Elif Özçelik (Student)]

Problem is that when I used your command or any command to install bcftools, it installs 1.9 instead of 1.14

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main

  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu

  bcftools           bioconda/linux-64::bcftools-1.9-ha228f0b_4

  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0

  c-ares             pkgs/main/linux-64::c-ares-1.17.1-h27cfd23_0

  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2

  curl               pkgs/main/linux-64::curl-7.78.0-h1ccaba5_0

  krb5               pkgs/main/linux-64::krb5-1.19.2-hac12032_0

  libcurl            pkgs/main/linux-64::libcurl-7.78.0-h0b77cf5_0

  libdeflate         bioconda/linux-64::libdeflate-1.0-h14c3975_1

  libedit            pkgs/main/linux-64::libedit-3.1.20210910-h7f8727e_0

  libev              pkgs/main/linux-64::libev-4.33-h7f8727e_1

  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17

  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17

  libnghttp2         pkgs/main/linux-64::libnghttp2-1.46.0-hce63b2e_0

  libssh2            pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1

  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17

  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2

  openssl            pkgs/main/linux-64::openssl-1.1.1l-h7f8727e_0

  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0

  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: done

Verifying transaction: done

Executing transaction: - 

[John Eppley]

You need to have conda-forge in your channels for bioconda to work properly:

https://bioconda.github.io/user/install.html#set-up-channels

I suspect the latest version of bfctools needs a dependency that's not in the main channel (and is only available in conda-forge). Run the three commands in the linked instructions:

    conda config --add channels defaults 

    conda config --add channels bioconda 

    conda config --add channels conda-forge

Then try your installation again.

[Ariel Balter]

That's a great point, and not well-documented! My .condarc is

```

channels:

    - conda-forge

    - bioconda

    - defaults

```

[Elif Özçelik (Student)]

thanks a lot, it worked.

--

Elif Özçelik

Undergraduate Student
Computer Science and Engineering
Molecular Biology, Genetics and Bioengineering

Sabanci University, Istanbul