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conda安装samtools

2021-05-26 14:59:36  阅读:730  来源: 互联网

标签:bin samtools lib anaconda3 so.1 conda hjb home 安装


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

OK


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

标签:bin,samtools,lib,anaconda3,so.1,conda,hjb,home,安装
来源: https://blog.csdn.net/geekfocus/article/details/117291158

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