\u6b64\u65b9\u6cd5\u662f\u7531\u90d1\u8d8a\u540c\u5b66\u63d0\u4f9b\u7684\u3002<\/p>\n
QIIME consists of native Python 2 code and additionally wraps many external applications. As a consequence of this pipeline architecture, QIIME has a lot of dependencies and can be very challenging to install.<\/p>\n
Paste the following into that file:<\/p>\n
\r\n[home_fengshuo_zeromq]\r\nname=The latest stable of zeromq builds (CentOS_CentOS-6)\r\ntype=rpm-md\r\nbaseurl=http:\/\/download.opensuse.org\/repositories\/home:\/fengshuo:\/zeromq\/CentOS_CentOS-6\/\r\ngpgcheck=1\r\ngpgkey=http:\/\/download.opensuse.org\/repositories\/home:\/fengshuo:\/zeromq\/CentOS_CentOS-6\/repodata\/repomd.xml.key\r\nenabled=1\r\n<\/pre>\nSave and exit that file<\/p>\n
1.2 Install the qiime-deploy dependencies on your machine<\/h2>\n
\r\nsudo yum groupinstall -y \"development tools\"\r\nsudo yum install -y ant compat-gcc-34-g77 java-1.6.0-openjdk java-1.6.0-openjdk-devel freetype freetype-devel zlib-devel mpich2 readline-devel zeromq zeromq-devel gsl gsl-devel libxslt libpng libpng-devel libgfortran mysql mysql-devel libXt libXt-devel libX11-devel mpich2 mpich2-devel libxml2 xorg-x11-server-Xorg dejavu* python-devel sqlite-devel tcl-devel tk-devel R R-devel ghc\r\n<\/pre>\n2. Installing requisite Python and R packages<\/h1>\n
\r\n# Installing sqlite-devel\r\nsudo yum install sqlite-devel \u2013y\r\n\r\n# Installing Python 2.7\r\nwget https:\/\/www.python.org\/ftp\/python\/2.7.8\/Python-2.7.8.tgz\r\ntar xf Python-2.7.8.tgz\r\ncd Python-2.7.8\r\n.\/configure --prefix=\/usr\r\nmake && make install\r\n\r\n# Install setuptools & pip\r\n# First get the setup script for Setuptools:\r\nwget https:\/\/bitbucket.org\/pypa\/setuptools\/raw\/bootstrap\/ez_setup.py\r\n# Then install it for Python 2.7 :\r\nsudo python2.7 ez_setup.py\r\n# Now install pip using the newly installed setuptools:\r\nsudo easy_install-2.7 pip\r\n# With pip installed you can now do things like this:\r\npip2.7 install [packagename]\r\n\r\n# Install virtualenv for Python 2.7\r\nsudo pip2.7 install virtualenv\r\n\r\n# Check the system Python interpreter version\r\npython --version\r\n# This will show Python 2.7.8\r\n\r\n# Maybe you will found yum can not be used this moment, because yum is associated with python2.6. Thus, we modified the yum conf files to use python2.6\r\nsudo vim \/usr\/bin\/yum\r\n# Replace \u201c#!\/usr\/bin\/python\u201d by \u201c#!\/usr\/bin\/python2.6\u201d\r\n<\/pre>\n\r\n# Installing R packages\r\n# Run R and execute the following commands\r\ninstall.packages(c('ape', 'biom', 'optparse', 'RColorBrewer', 'randomForest', 'vegan'))\r\nsource('http:\/\/bioconductor.org\/biocLite.R')\r\nbiocLite(c('DESeq2', 'metagenomeSeq'))\r\nq()\r\n<\/pre>\n3. Install the latest QIIME release and its base dependencies is with pip<\/h1>\n
\r\nsudo pip2.7 install numpy\r\nsudo pip2.7 install qiime -v\r\n# For Chines user, you may find the suspend of pip, as the limitation of network. For example, If FastTree cannot be download, you can download it by another port of internet, and then post the install package into your local address. Next step, Downloading the qiime-1.9.1.tar.gz and changing the description of FastTree in setpu.py. After you modified the qiime-1.9.1.tar.gz you can post it into your local address. Finally, run sudo pip2.7 install qiime \u2013v \u2013i [local address]\r\n\r\n# Installing QIIME 1.9.0's dependencies\r\n# Downloading the zip packages of \u2018qiime deploy\u2019 and \u2018qiime deploy conf\u2019 from Github\r\ncd\r\nunzip qiime-deploy-master.zip qiime-deploy-conf-master.zip\r\nmkdir ~\/qiime_software\r\ncd qiime-deploy-master\r\nsudo python2.7 qiime-deploy.py ~\/qiime_software\/ -f ~\/qiime-deploy-conf\/qiime\/qiime-1.9.1\/qiime.conf --force-remove-failed-dirs\r\n# After this step, it will display the list including \u2018Packages deployed successfully\u2019, \u2018Packages skipped\u2019 and \u2018Packages failed to deply\u2019\r\nsource ~\/qiime_software\/active.sh\r\nprint_qiime_config.py \u2013tf\r\n\r\n# If there are some packages were uninstalled, you should install them manually\r\n# For example, usearch and amplicannoise were failed to install.\r\n\r\n# Installing usearch manually\r\n# Visting http:\/\/www.drive5.com\/usearch\/download.html to download the USEARCH v5.2.236\r\n# Moving the binary file into \/usr\/bin and change the name as usearch, then chmod 755 [the binary file] \r\n\r\n# Installing usearch manually\r\n# Downloading the AmpliconNoiseV1.27.tar.gz\r\ntar -xvzf AmpliconNoiseV1.27.tar.gz\r\ncd AmpliconNoiseV1.27\r\nmake clean\r\nmake\r\nmake install\r\necho \"export PATH=$HOME\/AmpliconNoiseV1.27\/Scripts:$HOME\/AmpliconNoiseV1.27\/bin:$PATH\" >> $HOME\/.bashrc\r\necho \"export PYRO_LOOKUP_FILE=$HOME\/AmpliconNoiseV1.27\/Data\/LookUp_E123.dat\" >> $HOME\/.bashrc\r\necho \"export SEQ_LOOKUP_FILE=$HOME\/AmpliconNoiseV1.27\/Data\/Tran.dat\" >> $HOME\/.bashrc\r\n\r\n# PATH Environment Variable\r\necho \"export PATH=$HOME\/bin\/:$PATH\" >> $HOME\/.bashrc\r\nsource $HOME\/.bashrc\r\n\r\n# Finnaly verification\r\nsource ~\/qiime_software\/active.sh\r\nprint_qiime_config.py \u2013tf\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"\u6b64\u65b9\u6cd5\u662f\u7531\u90d1\u8d8a\u540c\u5b66\u63d0\u4f9b\u7684\u3002 QIIME consists of native P … \u7ee7\u7eed\u9605\u8bfb