conda管理软件遇到的莫名其妙的的库文件缺少
初学者会大量依赖于conda傻瓜式管理软件，在这里首先强推《生信技能树》团队的卖萌哥在2021新年伊始的公开课：
https://www.bilibili.com/video/BV1Yy4y117SX
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/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The following packages will be SUPERSEDED by a higher-priority channel: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/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The following packages will be SUPERSEDED by a higher-priority channel: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/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