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其它之前很多人都用过Conda,特别是生信科学家近两年都在用Bioconda,那叫一个妙不可言、根本停不下来。这里我郑重通知大家,Bioconda于今年6月2号正式发表于Nature Methods(IF=26.9)。吃水不忘挖井人,用过的写文章记得引用它。
Bioconda是生物软件库,可以利用Conda快速安装绝大多数生物学软件,让生物学家从复杂的版本和依赖关系中解脱出来,专心数据分析。
Bioconda主页:https://bioconda.github.io/
想查询要使用的软件及指定版本是否己被Bioconda收录,可访问 https://bioconda.github.io/recipes.html#recipes 查询:
上图看到查询qiime,发现目前bioconda已经有8744个软件及版本收录,qiime有1.9.1和1.8.0,大多数在Linux和OSX都可以使用。安装时可以指定版本,如不指定则安装最新版本。
查询到的软件名,可以点击进入
有详细的安装和升级说明,而且还有Docker镜像,即使你安装不成功,也可以使用Docker方式来使用软件。这一点非常重要,因为conda也会存在依赖关系无法解决的情况,或安装完仍存在问题。但Docker是不存在外部依赖问题的,成功率更高。
想使用Bioconda,你需要先安装Conda。
Conda是目前最方便的软件管理器,可以一键安装大多数生物学软件,让你从痛苦的依赖关系和包安装中解脱出来。常用的发行版有Anaconda,和miniconda两种。从字面上看就知道一个非常大,一个很小。这里推荐你空间大的选anaconda,想快速安装的选miniconda。
而且每个版本都有Python2和Python3的版本,这里我们选择python2的版本,对目前大多数软件兼容更好。
本教程演示使用的测试平台为Ubuntu 16.04,~/bin默认为自己的环境变量目录
# 创建并进入测试目录中的软件目录,请按个人习惯修改
mkdir -p ~/test/soft && cd ~/test/soft
下面Anaconda和Miniconda任选其一即可,这里推荐Miniconda更小巧。
# https://www.anaconda.com 下载Linux python2.7 5.1
wget -c https://repo.anaconda.com/archive/Anaconda2-5.2.0-Linux-x86_64.sh &
bash Anaconda2-5.2.0-Linux-x86_64.sh
# 安装过程同下面minicona
# 可选miniconda https://conda.io/miniconda.html
wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh
# Miniconda2 4.5.4
按提示Enter回车、输入yes同意许可协议、默认安装目录为~/miniconda2回车即可;安装结束后提示添加环境变量,一般选no,否则可能会破坏你之前安装的软件依赖关系。如果你是新用户,没什么软件可破坏的,请选yes添加以后使用更方便。
如上面选择no,以后想使用conda,还要执行下面一句话临时添加conda为环境变量
export PATH=/mnt/bai/yongxin/miniconda2/bin:$PATH
主要是添加bioconda频道,方便生物软件安装。添加清华的一系列镜像,加速下载,提高成功率。默认仓库不仅速度极慢,而且经常中断,国内镜像下载速度可达国外几百倍。
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
# 添加清华镜像加速下载
site=https://mirrors.tuna.tsinghua.edu.cn/anaconda
conda config --add channels ${site}/pkgs/free/
conda config --add channels ${site}/pkgs/main/
conda config --add channels ${site}/cloud/conda-forge/
conda config --add channels ${site}/pkgs/r/
conda config --add channels ${site}/cloud/bioconda/
conda config --add channels ${site}/cloud/msys2/
conda config --add channels ${site}/cloud/menpo/
conda config --add channels ${site}/cloud/pytorch/
conda install bowtie2
显示如下信息:
Solving environment: done
## Package Plan ##
environment location: /mnt/bai/yongxin/miniconda2
added / updated specs:
- bowtie2
The following packages will be downloaded:
package | build
---------------------------|-----------------
bowtie2-2.3.4.2 | py27h2d50403_0 13.6 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
certifi-2018.8.24 | py27_1 139 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-5.26.2 | h470a237_0 15.8 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates-2018.8.24 | ha4d7672_0 136 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl-1.0.2o | h470a237_1 3.5 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda-4.5.11 | py27_0 634 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
------------------------------------------------------------
Total: 33.8 MB
The following NEW packages will be INSTALLED:
bowtie2: 2.3.4.2-py27h2d50403_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
perl: 5.26.2-h470a237_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
The following packages will be UPDATED:
ca-certificates: 2018.03.07-0 --> 2018.8.24-ha4d7672_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi: 2018.4.16-py27_0 --> 2018.8.24-py27_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda: 4.5.4-py27_0 --> 4.5.11-py27_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl: 1.0.2o-h20670df_0 --> 1.0.2o-h470a237_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
Proceed ([y]/n)?
主要是该软件的依赖关系,及依赖关系下载地点,输入y
回车,等着安装完成即可。
对于依赖上百个软件和包的流程,一键安装成功,那叫一个字“爽”!轻松节约你原来几天的时间。
conda可以轻松安装众多宏基因组领域软件
# 宏基因组质控流程
conda install kneaddata
# humann2有参物种功能定量流程
conda install humann2
# grahplan树图
conda install graphlan
conda install export2graphlan
有时为了之前安装的软件依赖关系不被影响,或默认安装时无法满足依赖关系时,就需要新建虚拟环境,并指定版本来安装。以kneaddata为例,这是一个质控、去宿主和流程依赖很多。如果你原来是Python3,则需要虚拟环境中安装Python2.7才能运行成功。
conda create -n kneaddata kneaddata=0.6.1 python=2.7
显示安装的指定版本和依赖关系,这个不少吧,共31个软件和包,这要是之前自己装,可能3天都不一定搞得定。
## Package Plan ##
environment location: /mnt/bai/yongxin/miniconda2/envs/kneaddata
added / updated specs:
- kneaddata=0.6.1
- python=2.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-2.7.15 | h9fef7bc_0 13.9 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost-1.59.0 | py27_0 12.7 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo
krb5-1.14.6 | 0 4.0 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
blast-2.5.0 | h3727419_3 137.8 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
openssl-1.0.2p | h470a237_0 3.5 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bmtagger-3.101 | h470a237_4 7 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bmtool-3.101 | hfc679d8_2 64 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bmfilter-3.101 | hfc679d8_2 83 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
kneaddata-0.6.1 | py_2 406 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
readline-7.0 | haf1bffa_1 381 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trimmomatic-0.36 | 3 132 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
wheel-0.31.1 | py27_1 61 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bzip2-1.0.6 | h470a237_2 310 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses-6.1 | hfc679d8_1 1.2 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
extract_fullseq-3.101 | 3 8 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
sqlite-3.24.0 | h2f33b56_0 1.5 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
srprism-2.4.24 | h96824bc_3 457 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
pip-18.0 | py27_1 1.7 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-7.2.0 | h69d50b8_2 304 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib-1.2.11 | h470a237_3 93 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools-40.2.0 | py27_0 585 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trf-4.09 | 1 47 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
libstdcxx-ng-7.2.0 | hdf63c60_3 2.5 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz-5.2.4 | h470a237_1 328 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
samtools-1.7 | 1 1.0 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
libgcc-ng-7.2.0 | hdf63c60_3 6.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libssh2-1.8.0 | h5b517e9_2 240 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
curl-7.61.0 | h93b3f91_1 860 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tk-8.6.8 | 0 3.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fastqc-0.11.5 | 1 9.5 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
java-jdk-8.0.92 | 1 122.3 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
------------------------------------------------------------
Total: 325.3 MB
安装完成后提示如何打开、关闭新的环境
# 激活工作环境To activate this environment, use:
source activate kneaddata
#
# 关闭环境To deactivate an active environment, use:
source deactivate
#
conda list -n kneaddata
显示软件安装位置、依赖关系、版本和下载地址如下:
# packages in environment at /mnt/bai/yongxin/miniconda2/envs/kneaddata:
#
# Name Version Build Channel
blast 2.5.0 h3727419_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bmfilter 3.101 hfc679d8_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bmtagger 3.101 h470a237_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bmtool 3.101 hfc679d8_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
boost 1.59.0 py27_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo
bowtie2 2.3.4.2 py27h2d50403_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bzip2 1.0.6 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates 2018.8.24 ha4d7672_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi 2018.8.24 py27_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
curl 7.61.0 h93b3f91_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
extract_fullseq 3.101 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
fastqc 0.11.5 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
java-jdk 8.0.92 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
kneaddata 0.6.1 py_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
krb5 1.14.6 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc 7.2.0 h69d50b8_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng 7.2.0 hdf63c60_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libssh2 1.8.0 h5b517e9_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses 6.1 hfc679d8_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl 1.0.2p h470a237_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl 5.26.2 h470a237_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pip 18.0 py27_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python 2.7.15 h9fef7bc_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline 7.0 haf1bffa_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
samtools 1.7 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
setuptools 40.2.0 py27_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sqlite 3.24.0 h2f33b56_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
srprism 2.4.24 h96824bc_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
tk 8.6.8 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trf 4.09 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
trimmomatic 0.36 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
wheel 0.31.1 py27_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz 5.2.4 h470a237_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib 1.2.11 h470a237_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
Grüning, B., et al. (2018). “Bioconda: sustainable and comprehensive software distribution for the life sciences.” Nature Methods 15(7): 475-476. https://doi.org/10.1038/s41592-018-0046-7
生信软件的好帮手-bioconda https://mp.weixin.qq.com/s/nK1Kkf9lfZStoX25Y7SzHQ
生信分析平台搭建(七):bioconda https://mp.weixin.qq.com/s/ng8oNU81UQ6FtBqkyMGV5A
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