我有一个 conda 环境,其中安装了包括 bcftools 在内的软件包。我正在使用bcftools stats为我的 VCF 文件生成一些统计信息。然后,我想使用同样来自 bcftools的 plot-vcfstats绘制生成的统计信息。但是,当我在我的 conda 环境中安装 bcftools 时,该命令结果依赖于某些未安装的软件包。我运行时得到的输出plot-vcfstats
:
Parsing bcftools stats output: test.txt
Plotting graphs: python3 plot.py
Traceback (most recent call last):
File "plot.py", line 54, in <module>
import matplotlib as mpl
ModuleNotFoundError: No module named 'matplotlib'
The command exited with non-zero status 256:
python3 plot.py
matplotlib
可以使用 conda 轻松安装,所以我这样做了,但随后出现以下错误:
Parsing bcftools stats output: test.txt
Plotting graphs: python3 plot.py
Neither pdflatex or tectonic were found in your PATH, impossible to create a PDF at /home/nick/miniconda3/envs/variantcallingpipeline/bin/plot-vcfstats line 112.
main::error("Neither pdflatex or tectonic were found in your PATH, impossi"...) called at /home/nick/miniconda3/envs/variantcallingpipeline/bin/plot-vcfstats line 1934
main::create_pdf(HASH(0x7fffc2f047b0)) called at /home/nick/miniconda3/envs/variantcallingpipeline/bin/plot-vcfstats line 73
但是,我找不到安装pdflatex
和tectonic
依赖项的简单方法,甚至可能需要更多依赖项。所以,我想知道是否有一种简单的方法来安装plot-vcfstats
(或任何工具)的所有必需的依赖项,如果这一切都可以使用 conda。
编辑:我只是尝试安装pdflatex
并tectonic
通过:
conda install -c conda-forge texlive-core
这将错误更改为:
Parsing bcftools stats output: test.txt
Plotting graphs: python3 plot.py
Note: The xcolor.sty package not available, black and white tables only...
Creating PDF: pdflatex summary.tex >plot-vcfstats.log 2>&1
The command exited with non-zero status, please consult the output of pdflatex: .plot-vcfstats.log
at /home/nick/miniconda3/envs/test/bin/plot-vcfstats line 112.
main::error("The command exited with non-zero status, please consult the o"...) called at /home/nick/miniconda3/envs/test/bin/plot-vcfstats line 2206
main::create_pdf(HASH(0x7fffd8101f90)) called at /home/nick/miniconda3/envs/test/bin/plot-vcfstats line 73
日志文件包含以下内容:
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
kpathsea: Running mktexfmt pdflatex.fmt
Can't locate mktexlsr.pl in @INC (@INC contains: /home/nick/miniconda3/envs/test/share/tlpkg /home/nick/miniconda3/envs/test/share/texmf-dist/scripts/texlive /home/nick/.t_coffee/perl/lib/perl5 /home/nick/.t_coffee/perl/lib/perl5 /home/nick/miniconda3/envs/test/lib/perl5/5.32/site_perl /home/nick/miniconda3/envs/test/lib/perl5/site_perl /home/nick/miniconda3/envs/test/lib/perl5/5.32/vendor_perl /home/nick/miniconda3/envs/test/lib/perl5/vendor_perl /home/nick/miniconda3/envs/test/lib/perl5/5.32/core_perl /home/nick/miniconda3/envs/test/lib/perl5/core_perl .) at /home/nick/miniconda3/envs/test/bin/mktexfmt line 23.
BEGIN failed--compilation aborted at /home/nick/miniconda3/envs/test/bin/mktexfmt line 25.
I can't find the format file `pdflatex.fmt'!