conda安装samtools 报错

最新推荐文章于 2024-03-11 15:36:22 发布

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最新推荐文章于 2024-03-11 15:36:22 发布

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分类专栏： linux 文章标签： samtools conda

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本文讲述了samtools遇到libtinfow.so.5缺失错误，通过检查依赖并发现由于conda不同channel间的openssl版本冲突。提供了解决方案，包括软链接和调整conda配置，确保正确链接openssl 1.0.x版本以运行samtools 1.9。

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参考文档：
link1写的很棒
link2

error：

samtools: error while loading shared libraries: libtinfow.so.5: cannot open shared object file: No such file or directory

通过ldd查看samtools依赖了哪些工具。

$ ldd `which samtools`
        linux-vdso.so.1 =>  (0x00007ffdd0950000)
        libz.so.1 => /home/hjb_usr04/anaconda3/bin/../lib/libz.so.1 (0x00007f0885979000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f0885477000)
        libbz2.so.1.0 => /home/hjb_usr04/anaconda3/bin/../lib/libbz2.so.1.0 (0x00007f088595f000)
        liblzma.so.5 => /home/hjb_usr04/anaconda3/bin/../lib/liblzma.so.5 (0x00007f0885936000)
        libcurl.so.4 => /home/hjb_usr04/anaconda3/bin/../lib/libcurl.so.4 (0x00007f08858ac000)
        libcrypto.so.1.0.0 => not found
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f088525b000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f0884e8d000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f0885779000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f0884c85000)
        libssh2.so.1 => /home/hjb_usr04/anaconda3/bin/../lib/./libssh2.so.1 (0x00007f0885867000)
        libssl.so.1.1 => /home/hjb_usr04/anaconda3/bin/../lib/./libssl.so.1.1 (0x00007f08857d7000)
        libcrypto.so.1.1 => /home/hjb_usr04/anaconda3/bin/../lib/./libcrypto.so.1.1 (0x00007f08849b9000)
        libgssapi_krb5.so.2 => /home/hjb_usr04/anaconda3/bin/../lib/./libgssapi_krb5.so.2 (0x00007f0884966000)
        libkrb5.so.3 => /home/hjb_usr04/anaconda3/bin/../lib/./libkrb5.so.3 (0x00007f0884893000)
        libk5crypto.so.3 => /home/hjb_usr04/anaconda3/bin/../lib/./libk5crypto.so.3 (0x00007f08857bc000)
        libcom_err.so.3 => /home/hjb_usr04/anaconda3/bin/../lib/./libcom_err.so.3 (0x00007f08857b5000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f088468f000)
        libkrb5support.so.0 => /home/hjb_usr04/anaconda3/bin/../lib/././libkrb5support.so.0 (0x00007f08857a5000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f0884475000)

conda的各个channel之间冲突, 因此修改~/.condarc提高conda-forge的优先级

channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - defaults
show_channel_urls:true

可用方法：

This is because the samtools 1.9 depends on openssl 1.0.x (I hope the next version will support or just change the shared library name) and openssl 1.1.x was installed，if you must keep the openssl 1.1.x version, a possible solution is :
1. move to the /*Your_Path_of_conda/lib (for me ~/anaconda3/lib/) folder
2. give a soft link of "libcrypto.so.1.1" named "libcrypto.so.1.0.0" to cheat on the samtools

cd ./anaconda3/lib/
ll libcry*
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0

??conda install -c bioconda samtools openssl=1.0不起作用？