莫名其妙的conda管理软件的库文件缺少

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初学者会大量依赖于conda傻瓜式管理软件

默认代码

$ conda install -y -c bioconda salmon
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

environment location: /home/jmzeng/miniconda3/envs/rna

added / updated specs:
 - salmon

The following packages will be downloaded:

package | build
 ---------------------------|-----------------
 salmon-0.6.0 | 1 4.2 MB bioconda
 ------------------------------------------------------------
 Total: 4.2 MB

The following packages will be SUPERSEDED by a higher-priority channel:

salmon anaconda/cloud/bioconda --> bioconda

使用时候会报错:

$ salmon 
salmon: error while loading shared libraries: libboost_iostreams.so.1.60.0: cannot open shared object file: No such file or directory

修正代码


$ conda install -y -c conda-forge -c bioconda salmon
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

environment location: /home/jmzeng/miniconda3/envs/rna

added / updated specs:
 - salmon

The following packages will be downloaded:

package | build
 ---------------------------|-----------------
 ca-certificates-2020.12.5 | ha878542_0 137 KB conda-forge
 certifi-2020.12.5 | py37h89c1867_1 143 KB conda-forge
 openssl-1.1.1j | h7f98852_0 2.1 MB conda-forge
 ------------------------------------------------------------
 Total: 2.4 MB

The following packages will be SUPERSEDED by a higher-priority channel:

ca-certificates anaconda/cloud/conda-forge --> conda-forge
 certifi anaconda/cloud/conda-forge --> conda-forge
 openssl anaconda/cloud/conda-forge --> conda-forge

仍然是同样的报错:

先猜测是版本问题

$ conda search salmon 
Loading channels: done
# Name Version Build Channel 
salmon 0.5.1 0 anaconda/cloud/bioconda
salmon 0.6.0 0 anaconda/cloud/bioconda
salmon 0.6.0 1 anaconda/cloud/bioconda
salmon 0.6.0 boost1.60_1 anaconda/cloud/bioconda
salmon 0.6.0 boost1.60_2 anaconda/cloud/bioconda
salmon 0.7.2 boost1.60_2 anaconda/cloud/bioconda
salmon 0.7.2 boost1.60_3 anaconda/cloud/bioconda
salmon 0.7.2 boost1.61_3 anaconda/cloud/bioconda
salmon 0.8.0 boost1.60_0 anaconda/cloud/bioconda
salmon 0.8.0 boost1.61_0 anaconda/cloud/bioconda
salmon 0.8.1 0 anaconda/cloud/bioconda
salmon 0.8.2 0 anaconda/cloud/bioconda
salmon 0.8.2 1 anaconda/cloud/bioconda
salmon 0.9.0 0 anaconda/cloud/bioconda
salmon 0.9.1 0 anaconda/cloud/bioconda
salmon 0.9.1 1 anaconda/cloud/bioconda
salmon 0.10.0 1 anaconda/cloud/bioconda
salmon 0.10.1 1 anaconda/cloud/bioconda
salmon 0.10.2 1 anaconda/cloud/bioconda
salmon 0.11.0 h445c947_0 anaconda/cloud/bioconda
salmon 0.11.1 h445c947_0 anaconda/cloud/bioconda
salmon 0.11.2 h445c947_0 anaconda/cloud/bioconda
salmon 0.11.3 h86b0361_1 anaconda/cloud/bioconda
salmon 0.11.3 h86b0361_2 anaconda/cloud/bioconda
salmon 0.12.0 h86b0361_1 anaconda/cloud/bioconda
salmon 0.13.0 h86b0361_1 anaconda/cloud/bioconda
salmon 0.13.0 h86b0361_2 anaconda/cloud/bioconda
salmon 0.13.1 h86b0361_0 anaconda/cloud/bioconda
salmon 0.14.0 h86b0361_0 anaconda/cloud/bioconda
salmon 0.14.0 h86b0361_1 anaconda/cloud/bioconda
salmon 0.14.1 h86b0361_0 anaconda/cloud/bioconda
salmon 0.14.1 h86b0361_1 anaconda/cloud/bioconda
salmon 0.14.1 ha0cc327_2 anaconda/cloud/bioconda
salmon 0.14.2 ha0cc327_0 anaconda/cloud/bioconda
salmon 0.14.2 hf69c8f4_1 anaconda/cloud/bioconda
salmon 0.15.0 hf69c8f4_0 anaconda/cloud/bioconda
salmon 1.0.0 hf69c8f4_0 anaconda/cloud/bioconda
salmon 1.1.0 hf69c8f4_0 anaconda/cloud/bioconda
salmon 1.2.0 hf69c8f4_0 anaconda/cloud/bioconda
salmon 1.2.1 hf69c8f4_0 anaconda/cloud/bioconda
salmon 1.3.0 hf69c8f4_0 anaconda/cloud/bioconda
salmon 1.4.0 hf69c8f4_0 anaconda/cloud/bioconda

我就纳闷了，为什么这么多个不同版本的salmon，conda居然是默认安装 0.6.0 ，我勒个去，不是说默认安装最新的吗？

指定版本安装

conda install -y salmon=1.4.0 
## Package Plan ##

environment location: /home/jmzeng/miniconda3/envs/rna

added / updated specs:
 - salmon=1.4.0

The following packages will be downloaded:

package | build
 ---------------------------|-----------------
 libxml2-2.9.10 | hee79883_0 1.3 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
 salmon-1.4.0 | hf69c8f4_0 14.4 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
 ------------------------------------------------------------
 Total: 15.7 MB

The following NEW packages will be INSTALLED:

jemalloc anaconda/cloud/conda-forge/linux-64::jemalloc-5.2.1-h9c3ff4c_5

The following packages will be REMOVED:

boost-1.74.0-py37h6dcda5c_3
 boost-cpp-1.74.0-hc6e9bd1_2

The following packages will be UPDATED:

salmon bioconda::salmon-0.6.0-1 --> anaconda/cloud/bioconda::salmon-1.4.0-hf69c8f4_0

神奇的事情发生了，确实解决了问题:

$ salmon 
salmon v1.4.0

Usage: salmon -h|--help or 
 salmon -v|--version or 
 salmon -c|--cite or 
 salmon [--no-version-check] <COMMAND> [-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
​

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