有一些软件不应该是使用conda的默认安装

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自从我们运行了生物信息学奇迹产品《共享服务器》之后，遇到了大量的服务器使用场景的小白提问。怕大家误解以为是我们服务器问题，我只好亲力亲为尽可能的辅导大家生物信息学基础知识点，比如有一些软件不应该是使用conda的默认安装，否则就会出现如下所示的问题！

image-20231030220407943

如果你看官方文档：https://anaconda.org/bioconda/sra-tools

conda install -c bioconda sra-tools
conda install -c "bioconda/label/cf201901" sra-tools

上面的两个方式都是可以使用conda安装，但是默认安装的说 sra-tools-2.8.0 ：


The following packages will be downloaded:

package | build
 ---------------------------|-----------------
 ca-certificates-2023.08.22 | h06a4308_0 123 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
 openssl-1.1.1w | h7f8727e_0 3.7 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
 ------------------------------------------------------------
 Total: 3.9 MB

The following NEW packages will be INSTALLED:

sra-tools bioconda/linux-64::sra-tools-2.8.0-0

如果是简单的看这个软件的部分命令的帮助文档，会误以为软件是成功的，如下所示：

image-20231030215754989

但是实际上如果我们真正的使用它来下载，会出现如下所示的错误提示信息：

2023-10-30T14:01:52 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-10-30T14:01:52 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 ( !! The certificate is not correctly signed by the trusted CA )
2023-10-30T14:01:52 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module

小伙伴们看到了这样的报错就会很懵逼，但是我们遇到了太多了这样的求助！

但是如果我们安装最新版，也是看官方文档：https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit，我们通常是基于Ubuntu的Linux学徒：

cd ~/biosoft/
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.7/sratoolkit.3.0.7-ubuntu64.tar.gz
tar zxvf sratoolkit.3.0.7-ubuntu64.tar.gz 
cd sratoolkit.3.0.7-ubuntu64/bin
ls

然后使用最新版的

 ~/biosoft/sratoolkit.3.0.7-ubuntu64/bin/prefetch SRR8705087 --max-size 50G

就可以看到如下所示软件正确运行的提示：

2023-10-30T13:54:07 prefetch.3.0.7 int: buffer insufficient while reading uri within cloud module - cannot Get Cloud Location
2023-10-30T13:54:08 prefetch.3.0.7: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2023-10-30T13:54:09 prefetch.3.0.7: 1) Downloading 'SRR8705087'...
2023-10-30T13:54:09 prefetch.3.0.7: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2023-10-30T13:54:09 prefetch.3.0.7: Downloading via HTTPS...
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