2019-07-25 安装三代测序环境pacbio公司的工具全家
我参考这个文章安装pacbio全家桶，centos，总是不成功。
安装篇
推荐用conda安装pacbio公司的工具全家桶，方便而且不容易出各种诡异的问题， 同时建议采用我的代码，专门为pacbio的工具集建一个环境
conda create -n pb-assembly pb-assembly
# 启动
conda activate pb-assembly
作者：徐洲更
链接：https://www.jianshu.com/p/303ef83f5822
来源：简书
简书著作权归作者所有，任何形式的转载都请联系作者获得授权并注明出处。
wheel: 0.33.4-py37_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
xz: 5.2.4-h14c3975_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zlib: 1.2.11-h7b6447c_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: failed
ERROR conda.core.link:_execute(502): An error occurred while installing package 'https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda::pbgcpp-0.0.1-0'.
UnicodeDecodeError('ascii', '/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd:/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd/gatk-4.0.0.0:/home/Acer1/anaconda2/bin:/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd:/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd/gatk-4.0.0.0:/home/Acer1/anaconda2/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/Acer1/.local/bin:/home/Acer1/bin', 12, 13, 'ordinal not in range(128)')
Attempting to roll back.
Rolling back transaction: done
UnicodeDecodeError('ascii', '/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd:/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd/gatk-4.0.0.0:/home/Acer1/anaconda2/bin:/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd:/home/Acer1/\xe4\xb8\x8b\xe8\xbd\xbd/gatk-4.0.0.0:/home/Acer1/anaconda2/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/Acer1/.local/bin:/home/Acer1/bin', 12, 13, 'ordinal not in range(128)')
初步诊断会不会是py2.7 不识别中文路径导致乱码？
image.png
尝试升级3.0以上，装了anaconda3.0版本，再试，还是不行，一样的错误
google查找UnicodeDecodeError('ascii', ，解决方法乱七八糟，无用
换查找关键词 Executing transaction: failed ERROR conda.core.link:_execute(502): An error occurred while installing package UnicodeDecodeError('ascii',
解决方法：https://github.com/ContinuumIO/anaconda-issues/issues/8733
Have exactly the same issue (same error) on Windows 10. After reading the above, ran "conda update ipykernel" - it ran successfully. Then I ran "conda update --all" again. It seems to be working for me.
先运行conda update ipykernel
再运行 conda update --all
期间conda update --all时候遇到这样的问题，认为权限导致
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(656): An error occurred while uninstalling package 'https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda::gatk4-4.0.0.0-py27_0'.
Rolling back transaction: done
CondaMultiError: [Errno 13] Permission denied
()
换用su超级用户，再次 conda update --all，成功
再次运行
conda create -n pb-assembly pb-assembly
成功~！
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: -
# pbgcpp
##############################################################################
# #
# PacBio(R) tools distributed via Bioconda are: pre-release versions, not #
# necessarily ISO compliant, intended for Research Use Only and not for use #
# in diagnostic procedures, intended only for command-line users, and #
# possibly newer than the currently available SMRT(R) Analysis builds. While #
# efforts have been made to ensure that releases on Bioconda live up to the #
# quality that PacBio strives for, we make no warranty regarding any #
# Bioconda release. #
# #
# As PacBio tools distributed via Bioconda are not covered by any service #
# level agreement or the like, please *do not* contact a PacBio Field #
# Applications Scientist or PacBio Customer Service for assistance with any #
# Bioconda release. We instead provide an issue tracker for you to report #
# issues to us at: #
# #
# https://github.com/PacificBiosciences/pbbioconda #
# #
# We make no warranty that any such issue will be addressed, #
# to any extent or within any time frame. #
# #
# BSD 3-Clause Clear License #
# #
# Please see https://github.com/PacificBiosciences/pbbioconda for #
# information on License, Copyright and Disclaimer #
# #
##############################################################################
done
#
# To activate this environment, use
#
# $ conda activate pb-assembly
#
# To deactivate an active environment, use
#
# $ conda deactivate
又有看到这个解释
Installation
Information how to install conda and add the bioconda channel is available on https://bioconda.github.io/. Please verify that you have set up conda channel priorities according to https://bioconda.github.io/#set-up-channels. We strongly recommend you use Miniconda with the Python 2.7 backend, as PacBio packages are not Python 3 compatible yet.
Packages can be installed using following command:
> conda install -c bioconda package_name
Packages can be updated with:
> conda update package_name
In general, because conda only performs the smallest set of updates in order to satisfy the dependency graph, it is strongly advised to always update the environment as a whole afterwards:
> conda update --all
In order to avoid stale dependencies in the dependency graph.
好吧，，我错了，后知后觉
