search

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
780 stars 165 forks source link

PackagesNotFoundError #308

Open kbchoi-jax opened 6 years ago

kbchoi-jax commented 6 years ago

salmon is found from bioconda but ...

$ conda search salmon
Loading channels: done
# Name                  Version           Build  Channel
salmon                    0.5.1               0  bioconda
salmon                    0.6.0               0  bioconda
salmon                    0.6.0               1  bioconda
salmon                    0.6.0     boost1.60_1  bioconda
salmon                    0.6.0     boost1.60_2  bioconda
salmon                    0.7.2     boost1.60_2  bioconda
salmon                    0.7.2     boost1.60_3  bioconda
salmon                    0.7.2     boost1.61_3  bioconda
salmon                    0.8.0     boost1.60_0  bioconda
salmon                    0.8.0     boost1.61_0  bioconda
salmon                    0.8.1               0  bioconda
salmon                    0.8.2               0  bioconda
salmon                    0.8.2               1  bioconda
salmon                    0.9.0               0  bioconda
salmon                    0.9.1               0  bioconda
salmon                    0.9.1               1  bioconda
salmon                   0.10.0               1  bioconda
salmon                   0.10.1               1  bioconda
salmon                   0.10.2               1  bioconda
salmon                   0.11.0      h445c947_0  bioconda
salmon                   0.11.1      h445c947_0  bioconda
salmon                   0.11.2      h445c947_0  bioconda
salmon                   0.11.3      h86b0361_1  bioconda
salmon                   0.11.3      h86b0361_2  bioconda

When I try to install, I get PackageNotFoundError.

$ conda create -n salmon salmon=0.11.3
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - salmon=0.11.3
  - jemalloc[version='>=5.1.0']
  - salmon=0.11.3
  - libcxx

Current channels:

  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-64
  - https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

It is weird because I am installing on linux64.

$ lsb_release -a
LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description:    CentOS release 6.5 (Final)
Release:    6.5
Codename:   Final

Any help would be greatly appreciated.

ShaowenJ commented 5 years ago

I have a similar issue, does anyone know how to fix this? Many thanks

Peter-J-Freeman commented 5 years ago

Hi all,

bit of a manual workaround, but for each missing package I searched anaconda https://anaconda.org/, downloaded the package manually from downloads then installed the latest build of salmon using

conda install -c bioconda/label/main salmon

Hope this helps