加载中…16s_rRNA分析软件---QIIME精简安装--2014.12.31(更新)
(2013-01-21 11:11:16)| 分类： 生物信息学 |
QIIME （Quantitative Insights Into Microbial
Ecology）是一个专门针对于微生物群落的分析管道，可以进行OTU,以及多样性分析，等等。拥有处理16s
rRNA所需要的软件并呈现相应的处理结果。所谓分析管道必是集成软件，QIIME也不例外。因此安装起来比较麻烦。而且根据网站（http://qiime.org/）上给出主流的安装说明，需要将分析软件一个一个进行安装，非常不便.安装安装参考：https://github.com/qiime/qiime-deploy
git clone
git://github.com/qiime/qiime-deploy.git
git clone git://github.com/qiime/qiime-deploy-conf.git
cd qiime-deploy/
python qiime-deploy.py $HOME/qiime_software/ -f
$HOME/qiime-deploy-conf/qiime-1.8.0/qiime.conf
--force-remove-failed-dirs
source $HOME/.bashrc
注意：这种安装过程中往往会遇到很多软件是安装不成功的而且非常的耗费时间，前面提到qiime是一个集成的东西所以很多东西你用不到或者原来你的电脑上有。此外安装不成功的原因还有qiime软件自身提供的软件下载链接是被国内屏蔽的所以即使你能上网也下载安装不了。另外耗费时间比较长的一个原因是qiime给出的相关软件链接本身软件比较大，但是下载速度很慢。
为了实现尽快安装，请手动自行下载三个数据：
core_set_aligned.fasta.imputed
lanemask_in_1s_and_0s
gg_13_8_otus.tar.gz（下载并解压）
此外只下载基本的分析软件，剩下的可选的软件就不要安装了，这里需要修改的实际上是：$HOME/qiime-deploy-conf/qiime-1.8.0/qiime.conf
这里我提供一个我使用的一个范例，主要是修改了下载的软件种类以及软件下载的路径：
##############################################################################
#
# qiime.conf
#
# qiime-deploy configuration file
# This file specifies the applications to download and
deploy.
#
# This file contains a single [global] section and a single
[dependencies]
# section as well as any number of data or application
sections. Each section
# must have a unique name. Data sections must begin with
data-
#
# See the OPTIONS for a description of each option.
#
##############################################################################
[dependencies]
commands: gcc, g++, java, javac, ant
[global]
log-level: INFO
max-deploy-threads: 6
append-environment-to-bashrc: yes
append-environment-to-bashprofile: no
[python]
version: 2.7.3
build-type: autoconf
release-file-name: Python-2.7.3.tgz
set-environment-variables-value:
ATLAS=None,BLAS=None,LAPACK=None
release-location:
http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tgz
relative-directory-add-to-path: bin
autoconf-make-options: -j4
autoconf-configure-options: --enable-shared
--enable-unicode=ucs2 --enable-unicode=ucs4
set-environment-variables-deploypath:
LD_LIBRARY_PATH=lib
[numpy]
version: 1.7.1
build-type: python-distutils
release-file-name: numpy-1.7.1.tar.gz
release-location:
http://sourceforge.net/projects/numpy/files/NumPy/1.7.1/numpy-1.7.1.tar.gz
deps: python
[matplotlib]
version: 1.3.1
build-type: python-distutils
release-file-name: matplotlib-1.3.1.tar.gz
release-location:
https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.3.1.tar.gz
deps: numpy
[setuptools]
version: 0.6c11
build-type: python-distutils
release-file-name: setuptools-0.6c11.tar.gz
release-location:
http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz
deps: python
[pyqi]
version: 0.3.1
build-type: python-distutils
release-file-name: pyqi-0.3.1.tar.gz
release-location:
https://pypi.python.org/packages/source/p/pyqi/pyqi-0.3.1.tar.gz
relative-directory-add-to-path: bin
deps: python, setuptools
[biom-format]
version: 1.3.1
build-type: python-distutils
release-file-name: biom-format-1.3.1.tar.gz
release-location:
https://pypi.python.org/packages/source/b/biom-format/biom-format-1.3.1.tar.gz
relative-directory-add-to-path: bin
deps: python, numpy, pyqi
[sphinx]
version: 1.0.4
build-type: python-distutils
release-file-name: Sphinx-1.0.4.tar.gz
release-location:
http://pypi.python.org/packages/source/S/Sphinx/Sphinx-1.0.4.tar.gz#md5=d4067e42e75525ecf108ece471ce97bb
deps: python, setuptools
[qcli]
version: 0.1.0
build-type: python-distutils
release-file-name: qcli-0.1.0.tar.gz
release-location:
ftp://thebeast.colorado.edu/pub/qcli-releases/qcli-0.1.0.tar.gz
relative-directory-add-to-path: bin
deps: python
[emperor]
version: 0.9.3
build-type: python-distutils
release-file-name: emperor-0.9.3.tar.gz
release-location:
https://pypi.python.org/packages/source/e/emperor/emperor-0.9.3.tar.gz
relative-directory-add-to-path: bin
deps: numpy, qcli, setuptools
[pycogent]
version: 1.5.3
build-type: python-distutils
release-file-name: PyCogent-1.5.3.tgz
set-environment-variables-value: TEST_DB=1
copy-source-to-final-deploy: yes
release-location:
http://downloads.sourceforge.net/project/pycogent/PyCogent/1.5.3/PyCogent-1.5.3.tgz
deps: numpy
set-environment-variables-deploypath: PYCOGENT=./
[pynast]
version: 1.2.2
build-type: python-distutils
release-file-name: pynast-1.2.2.tar.gz
release-location:
https://pypi.python.org/packages/source/p/pynast/pynast-1.2.2.tar.gz
relative-directory-add-to-path: bin
deps: pycogent
[fasttree]
version: 2.1.3
build-type: c-file
release-file-name: FastTree-2.1.3.c
release-location:
http://www.microbesonline.org/fasttree/FastTree-2.1.3.c
c-file-compile-options: -lm
exe-name: FastTree
relative-directory-add-to-path: .
[qiime]
version: 1.8.0
build-type: python-distutils
release-file-name: qiime-1.8.0.tar.gz
release-location:
https://pypi.python.org/packages/source/q/qiime/qiime-1.8.0.tar.gz
relative-directory-add-to-path: bin
copy-source-to-final-deploy: yes
deps: pycogent, matplotlib
set-environment-variables-deploypath:
QIIME=./,PYTHONPATH=lib/
python-install-options: --install-scripts=bin/
--install-purelib=lib/
[rdpclassifier]
version: 2.2
build-type: copy
release-file-name: rdp_classifier_2.2.zip
unzipped-name: rdp_classifier_2.2
release-location:
http://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip
relative-directory-add-to-path: .
set-environment-variables-deploypath:
RDP_JAR_PATH=rdp_classifier-2.2.jar
[uclust]
version: 1.2.22
build-type: custom
release-file-name: uclustq1.2.22_i86linux64
release-location:
http://drive5.com/uclust/uclustq1.2.22_i86linux64
relative-directory-add-to-path: .
[gdata]
version: 2.0.17
build-type: python-distutils
release-file-name: gdata-2.0.17.tar.gz
release-location:
https://pypi.python.org/packages/source/g/gdata/gdata-2.0.17.tar.gz
deps: python
[sourcetracker]
version: 0.9.5
build-type: copy
release-file-name: sourcetracker-0.9.5.tar.gz
release-location:
http://sourceforge.net/projects/sourcetracker/files/sourcetracker-0.9.5.tar.gz
relative-directory-add-to-path: .
set-environment-variables-deploypath:
SOURCETRACKER_PATH=.
怎么样是不是少了很多。除了修改这个文件外其它的安装不变。另外当然由于三个数据你是自己下载的，下载完成后你需要修改下
qiime_config这个配置文件里的三个数据的路径。
2:运行出错：
from pylab import rc, axis, title, axes, pie, figlegend, clf,
savefig, figure\
问题出在pylab上，可以查看你运行的程序等源代码，并进行修改，网址：
https://github.com/Ecogenomics/GroopM/pull/20/commits/e84be53f583db740d5da5c7108f613044f0788ae
主要是pylab的问题。
3:参考数据下载：https://github.com/ekopylova/OTU-clustering
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