DeepVariant安裝
官方首推用docker裝，沒有root權(quán)限裝個錘子；然后是從源碼裝，源碼是基于Ubuntu的，我用的是CentOS；實(shí)在不行就用二進(jìn)制文件裝，我菜，我不會。
image-20211221164021047.png
最后發(fā)現(xiàn)可以用conda裝。
然后經(jīng)歷了一個晚上，一個上午，以及一個中午的自閉后，通過換環(huán)境、換源、換版本。。。等各種騷操作，最后在晚飯前終于成功了。
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另外，裝好后我一直用官方寫的run_deepvariant來測試，一直找不到命令，以為沒裝上，就又用conda裝了一遍，顯示已經(jīng)裝好。。。。再次自閉。（期間還請教了同學(xué)，說用docker裝成功了，但我沒root權(quán)限，docker也不會）
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后來去github上，找到了同樣問題的人。
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原來deepvariant的docker版本和conda版本命令不一樣。。。。我自閉了?。?
所以接下來說一說怎么用conda裝deepvariant
首先用conda搜一下有哪些版本的deepvariant以及需要的python版本
$conda search deepvariant
Loading channels: done
# Name Version Build Channel
deepvariant 0.4.1 np113py27_0 anaconda/cloud/bioconda
deepvariant 0.4.1 np113py27_1 anaconda/cloud/bioconda
deepvariant 0.6.0 py27_0 anaconda/cloud/bioconda
deepvariant 0.6.1 py27_0 anaconda/cloud/bioconda
deepvariant 0.6.1 py27h5d9141f_2 anaconda/cloud/bioconda
deepvariant 0.6.1 py27h5d9141f_3 anaconda/cloud/bioconda
deepvariant 0.7.0 py27h5d9141f_0 anaconda/cloud/bioconda
deepvariant 0.7.1 py27h5d9141f_0 anaconda/cloud/bioconda
deepvariant 0.7.2 py27h5d9141f_0 anaconda/cloud/bioconda
deepvariant 0.7.2 py27h5d9141f_1 anaconda/cloud/bioconda
deepvariant 0.8.0 py27h7333d49_0 anaconda/cloud/bioconda
deepvariant 0.9.0 py27h7333d49_0 anaconda/cloud/bioconda
deepvariant 0.10.0 py27h7333d49_0 anaconda/cloud/bioconda
deepvariant 0.10.0 py36h7333d49_1 anaconda/cloud/bioconda
deepvariant 0.10.0 py36h7333d49_2 anaconda/cloud/bioconda
deepvariant 0.10.0 py36h7333d49_3 anaconda/cloud/bioconda
deepvariant 0.10.0 py36hf5a246b_4 anaconda/cloud/bioconda
deepvariant 1.0.0 py36hf3e76ba_1 anaconda/cloud/bioconda
deepvariant 1.0.0 py36hf3e76ba_2 anaconda/cloud/bioconda
deepvariant 1.0.0 py36hf3e76ba_3 anaconda/cloud/bioconda
deepvariant 1.0.0 py36hf5a246b_0 anaconda/cloud/bioconda
deepvariant 1.1.0 py36hf3e76ba_0 anaconda/cloud/bioconda
deepvariant 1.1.0 py36hf3e76ba_1 anaconda/cloud/bioconda
deepvariant 1.1.0 py36hf3e76ba_2 anaconda/cloud/bioconda
deepvariant 1.2.0 py36hf3e76ba_0 anaconda/cloud/bioconda
deepvariant 1.3.0 py36hf3e76ba_0 anaconda/cloud/bioconda
我決定裝最新的1.3.0，需要python3.6。
所以新建一個python3.6的環(huán)境
conda create -name py3.6 python=3.6
PS：我在新建環(huán)境時(shí)也遇到了bug，一直顯示無法找到python3.6的包，最后是換源才解決的，來看一下我現(xiàn)在用的源
$cat ~/.condarc
ssl_verify: true
channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/pro
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/pro
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/r
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/free
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
- https://mirrors.ustc.edu.cn/anaconda/cloud/menpo/
- https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
- https://mirrors.ustc.edu.cn/anaconda/cloud/msys2/
- https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
- https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
- https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
- conda-forge
- defaults
show_channel_urls: true
default_channels:
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/r
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
custom_channels:
conda-forge: https://mirrors.bfsu.edu.cn/anaconda/cloud
msys2: https://mirrors.bfsu.edu.cn/anaconda/cloud
bioconda: https://mirrors.bfsu.edu.cn/anaconda/cloud
menpo: https://mirrors.bfsu.edu.cn/anaconda/cloud
pytorch: https://mirrors.bfsu.edu.cn/anaconda/cloud
pytorch-lts: https://mirrors.bfsu.edu.cn/anaconda/cloud
simpleitk: https://mirrors.bfsu.edu.cn/anaconda/cloud
搭建好環(huán)境后就直接安裝
conda install -c bioconda deepvariant=1.3.0
安裝好后用以下幾個命令測試是否安裝成功，能彈出命令用法說明安裝成功
$dv_make_examples.py
usage: dv_make_examples.py [--cores CORES] --sample SAMPLE --ref REF --reads
READS [--regions REGIONS] --logdir LOGDIR
--examples EXAMPLES [--gvcf GVCF] [-h]
dv_make_examples.py: error: the following arguments are required: --sample, --ref, --reads, --logdir, --examples
$dv_call_variants.py
usage: dv_call_variants.py [--cores CORES] --outfile OUTFILE --examples
EXAMPLES --sample SAMPLE
[--model {hybrid,pacbio,wes,wgs}] [-h]
dv_call_variants.py: error: the following arguments are required: --outfile, --examples, --sample
$dv_postprocess_variants.py
usage: dv_postprocess_variants.py --ref REF --infile INFILE --outfile OUTFILE
[--gvcf_infile GVCF_INFILE]
[--gvcf_outfile GVCF_OUTFILE] [-h]
dv_postprocess_variants.py: error: the following arguments are required: --ref, --infile, --outfile
最后，conda YYDS?。。?br> 希望下一個沒有Root權(quán)限需要裝DeepVariant的人不要像我一樣自閉?。?！
