conda安装samtools

2021-05-26 14:59:36 阅读：690 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

??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

本站声明： 1. iCode9 技术分享网（下文简称本站）提供的所有内容，仅供技术学习、探讨和分享；
2. 关于本站的所有留言、评论、转载及引用，纯属内容发起人的个人观点，与本站观点和立场无关；
3. 关于本站的所有言论和文字，纯属内容发起人的个人观点，与本站观点和立场无关；
4. 本站文章均是网友提供，不完全保证技术分享内容的完整性、准确性、时效性、风险性和版权归属；如您发现该文章侵犯了您的权益，可联系我们第一时间进行删除；
5. 本站为非盈利性的个人网站，所有内容不会用来进行牟利，也不会利用任何形式的广告来间接获益，纯粹是为了广大技术爱好者提供技术内容和技术思想的分享性交流网站。

ICode9

conda安装samtools