panpop 安装

[zgliu2000]

郑老师你好，我在Linux上使用conda进行安装panpop 时出现了报错，进行到这一步cpanm Tie::CharArray，显示Tie::CharArray is up to date. (1.00)请问是什么什么原因造成 ？应该怎么解决这个问题

[starskyzheng]

可以运行run_PART.pl试试，看看有报错么

[zgliu2000]

当我运行PART_run.pl  出现了下面的错误 Can't locate read_config.pm in @INC (you may need to install the read_config module) @.*** contains: /ngsproject/zgliu/tools/panpop/bin/../lib /ngsproject/zgliu/miniforge-pypy3/lib/perl5/5.32/site_perl /ngsproject/zgliu/miniforge-pypy3/lib/perl5/site_perl /ngsproject/zgliu/miniforge-pypy3/lib/perl5/5.32/vendor_perl /ngsproject/zgliu/miniforge-pypy3/lib/perl5/vendor_perl /ngsproject/zgliu/miniforge-pypy3/lib/perl5/5.32/core_perl /ngsproject/zgliu/miniforge-pypy3/lib/perl5/core_perl .) at /ngsproject/zgliu/tools/panpop/bin/PART_run.pl line 33. BEGIN failed--compilation aborted at /ngsproject/zgliu/tools/panpop/bin/PART_run.pl line 33.

------------------ 原始邮件 ------------------ 发件人: "starskyzheng/panpop" @.>; 发送时间: 2024年10月5日(星期六) 晚上10:50 @.>; @.**@.>; 主题: Re: [starskyzheng/panpop] panpop 安装 (Issue #75)

可以运行run_PART.pl试试，看看有报错么

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[starskyzheng]

/ngsproject/zgliu/tools/panpop/bin/../lib 这文件夹里有啥？

[zgliu2000]

 Identity.pm -rw-rw-r-- 1 zgliu zgliu 4.7K Oct  6 11:45 prase_vcf.pm -rw-rw-r-- 1 zgliu zgliu 2.4K Oct  6 11:45 read_config.pm -rw-rw-r-- 1 zgliu zgliu  31K Oct  6 11:45 realign_alts.pm -rw-rw-r-- 1 zgliu zgliu 7.4K Oct  6 11:45 zzBed.pm -rw-rw-r-- 1 zgliu zgliu 2.3K Oct  6 11:45 zzIO.pm -rw-rw-r-- 1 zgliu zgliu 7.8K Oct  6 11:45 zzmcl.pm

------------------ 原始邮件 ------------------ 发件人: "starskyzheng/panpop" @.>; 发送时间: 2024年10月6日(星期天) 下午2:27 @.>; @.**@.>; 主题: Re: [starskyzheng/panpop] panpop 安装 (Issue #75)

/ngsproject/zgliu/tools/panpop/bin/../lib 这文件夹里有啥？

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[zgliu2000]

现在又出现了新的错误Can't locate YAML.pm in @INC (you may need to install the YAML module) @.*** contains: /ngsproject/zgliu/tools/panpop/bin/../lib /ngsproject/zgliu/miniforge-pypy3/envs/panpop/lib/perl5/5.32/site_perl /ngsproject/zgliu/miniforge-pypy3/envs/panpop/lib/perl5/site_perl /ngsproject/zgliu/miniforge-pypy3/envs/panpop/lib/perl5/5.32/vendor_perl /ngsproject/zgliu/miniforge-pypy3/envs/panpop/lib/perl5/vendor_perl /ngsproject/zgliu/miniforge-pypy3/envs/panpop/lib/perl5/5.32/core_perl /ngsproject/zgliu/miniforge-pypy3/envs/panpop/lib/perl5/core_perl .) at /ngsproject/zgliu/tools/panpop/bin/../lib/read_config.pm line 29. BEGIN failed--compilation aborted at /ngsproject/zgliu/tools/panpop/bin/../lib/read_config.pm line 29. Compilation failed in require at /ngsproject/zgliu/tools/panpop/bin/PART_run.pl line 33. BEGIN failed--compilation aborted at /ngsproject/zgliu/tools/panpop/bin/PART_run.pl line 33.

------------------ 原始邮件 ------------------ 发件人: "starskyzheng/panpop" @.>; 发送时间: 2024年10月6日(星期天) 下午2:27 @.>; @.**@.>; 主题: Re: [starskyzheng/panpop] panpop 安装 (Issue #75)

/ngsproject/zgliu/tools/panpop/bin/../lib 这文件夹里有啥？

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[starskyzheng]

这个包应该在conda里已经安装了。您可以试试重新安装一遍。 或者，您可以看看目前的perl是不是conda环境的，然后可以清空PERL5LIB变量试试:unset PERL5LIB

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