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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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plot-vcfstats error #2024

Closed Seif-el-din closed 10 months ago

Seif-el-din commented 10 months ago

So, hi. I have been facing a problem with the plot-vcfstats function and was hoping anyone could help.

When I run the function, the following error message pops up:

Plotting graphs: python3 plot.py /home/seif_el_din/Mapping/plot.py:234: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead. cm = mpl.cm.get_cmap('autumn') Neither pdflatex or tectonic were found in your PATH, impossible to create a PDF at /usr/bin/plot-vcfstats line 112. main::error("Neither pdflatex or tectonic were found in your PATH, impossi"...) called at /usr/bin/plot-vcfstats line 1934 main::create_pdf(HASH(0x5584c2466d28)) called at /usr/bin/plot-vcfstats line 73

So like what should I do to resolve this issue? Should I download some package or what? Thank you in advance.

pd3 commented 10 months ago

Hi, this has been addressed a while ago, https://github.com/samtools/bcftools/issues/1878 and https://github.com/daviesrob/bcftools/commit/3298b7c7ba6b98de3b3fe7d448b88ef77b0b0118

Please use the latest version which can be obtained here https://github.com/samtools/bcftools/blob/develop/misc/plot-vcfstats

Seif-el-din commented 10 months ago

Sorry, seems like I missed that issue. Thanks a lot!

Edit: I'm so sorry but I can't seem to get it to work. I tried this wget https://github.com/samtools/bcftools/blob/3b24f36e0995f76bd6d71e854613f869fe6d50d1/misc/plot-vcfstats and wget https://raw.githubusercontent.com/samtools/bcftools/develop/misc/plot-vcfstats in the linux terminal on my windows laptop Yet the problem persists. I am still new to linux and the whole packages thing so I don't even know if this is the right way to download the latest version😅. So if you could tell me about how to download it, it would be greatly appreciated. Again thank you so much. @pd3

pd3 commented 10 months ago

If you follow the link above, on the github there is the link 'raw' which allows to download the file directly: https://raw.githubusercontent.com/samtools/bcftools/develop/misc/plot-vcfstats