linux学习100篇38：转录组分析用软件及安装salmon

安装

(rnaseq) root 11:55:29 ~
$ conda install -y salmon
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /root/miniconda3/envs/rnaseq

  added / updated specs:
    - salmon


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    boost-cpp-1.74.0           |       h312852a_4        16.3 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    jemalloc-5.2.1             |       h9c3ff4c_5         1.7 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    salmon-1.5.0               |       h84f40af_0         5.6 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    tbb-2020.2                 |       h4bd325d_4         1.5 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:        25.0 MB

The following NEW packages will be INSTALLED:

  boost-cpp          anaconda/cloud/conda-forge/linux-64::boost-cpp-1.74.0-h312852a_4
  jemalloc           anaconda/cloud/conda-forge/linux-64::jemalloc-5.2.1-h9c3ff4c_5
  salmon             anaconda/cloud/bioconda/linux-64::salmon-1.5.0-h84f40af_0
  tbb                anaconda/cloud/conda-forge/linux-64::tbb-2020.2-h4bd325d_4



Downloading and Extracting Packages
jemalloc-5.2.1       | 1.7 MB    | ######################################## | 100% 
tbb-2020.2           | 1.5 MB    | ######################################## | 100% 
salmon-1.5.0         | 5.6 MB    | ######################################## | 100% 
boost-cpp-1.74.0     | 16.3 MB   | ######################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rnaseq) root 11:57:05 ~

查看

(rnaseq) root 11:57:05 ~
$ salmon --help
salmon v1.5.0

Usage:  salmon -h|--help or 
        salmon -v|--version or 
        salmon -c|--cite or 
        salmon [--no-version-check]  [-h | options]

Commands:
     index      : create a salmon index
     quant      : quantify a sample
     alevin     : single cell analysis
     swim       : perform super-secret operation
     quantmerge : merge multiple quantifications into a single file
(rnaseq) root 11:58:03 ~
$ salmon
salmon v1.5.0

Usage:  salmon -h|--help or 
        salmon -v|--version or 
        salmon -c|--cite or 
        salmon [--no-version-check]  [-h | options]

Commands:
     index      : create a salmon index
     quant      : quantify a sample
     alevin     : single cell analysis
     swim       : perform super-secret operation
     quantmerge : merge multiple quantifications into a single file
(rnaseq) root 11:58:44 ~