TCGA_简单上手网站

  • UALCAN —> 可查看TCGA中相关基因,生存曲线,差异表达啥的
  • cBioPortal —-> 可查看TCGA中差异表达的基因
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clusterProfiler_github版本安装

#R-3.3.1,失败,因为最后安装强制要求了R的高版本
#镜像选择0-cloud
#install.packages("installr")
#library(installr)
#用于将之前的R包迁移到新的R中
#copy.packages.between.libraries(from="D:/R/R-3.3.1/library",to="D:/R/R-3.5.2/library",ask=T,keep_old=T,do_NOT_override_packages_in_new_R=T)
#install.packages("rlang")
#install.packages("debugme")
#install.packages("git2r")
#install.packages("devtools")
#若报ERROR: dependency 'pkgload' is not available for package 'devtools',则手动下载pkgload进行安装
#报地址https://cran.r-project.org/bin/windows/contrib/3.6/pkgload_1.0.2.zip
#包介绍地址https://cran.r-project.org/web/packages/pkgload/index.html
#install_github("GuangchuangYu/enrichplot") ===>要求R大于3.5.1
#install_github("GuangchuangYu/clusterProfiler") ====>要求R大于3.4

#R版本必须是3.5.1以上
install.packages("devtools")
library(devtools)
#需要安装Rtools,网址:https://cran.r-project.org/bin/windows/Rtools/
install_github("GuangchuangYu/enrichplot")
install_github("GuangchuangYu/clusterProfiler")
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免疫荧光实验

撒云俐实验笔记

  • 1:6孔板种细胞并转染 (6 x 10^5 cell/孔)
  • 2:36h后,将细胞种到12孔板中,(种细胞前,用灭过菌的镊子将细胞怕片放到12孔板中,种2 x 10^5 cell/孔)
  • 3:待细胞完全贴壁值 70%~80% 后,加药处理24h
  • 4:24h后,沿培养基12孔板壁加 1 x $ PBS(预先恢复至室温),清洗3遍
  • 5:弃1 x PBS,加 4% 多聚甲醛,室温静置固定20分钟,1 x PBS 洗2次(5分钟/次)
  • 6:加0.5% TritonX-100,1ml/孔,室温静置20分钟。1 x PBS洗3次,3分钟/次
  • 7:封闭:去除玻片,正面朝上放到另一新的12孔板中,每孔加800微升3%BSA封闭1h
  • 8:孵一抗:吸去封闭液,每片滴加足量稀释的一抗(用0.1%BSA配置),加盖湿盒,4摄氏度 过夜孵育(一抗稀释比详见说明书)
  • 9:吸去一抗,每孔加1mL 1 x PBS清洗,放在水平摇床上清洗,5分钟/次(共3次),孵二抗(二抗用之前离心,不要将沉淀吸出),室温避光孵育1小时(1:400)荧光二抗,用0.1%BSA配置,PBST清洗3次(3分钟/次)
  • 10(复染核):滴加DAPI(1mg/ml)避光孵育5分钟后,PBST洗4次,5min/次
  • 11:(封片拍照):将玻片正面向下倒扣在载玻片上,四周用指甲油固定,待干涸后,可现在普通荧光显微镜下观察是否有荧光,再用激光共聚焦显微镜观察

由于wordpress的markdown不好用,附一个用印象笔记写的链接:撒云俐实验笔记

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TCGA和dbGaP申请中的注意事项(SAM更新是否需要缴费)

  • SAM的renew不用交费,所以收到的所有关于缴费的邮件都是假的!
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GATK4_Spark版本_虚拟机并行计算测试

GATK4架构总览

Spark_Hadoop的GATK4,在后台自动进行了数据的切割
CPU利用率大约为250%-305%(4核心)

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GATK_FPGA加速器驱动安装

#Installing Required OS Packages and Components
sudo yum groupinstall 'Development and Creative Workstation'
sudo yum groupinstall 'Additional Develpment'
sudo yum groups mark install "Compatibility Libraries"
sudo yum groupinstall 'Development Tools' --setopt=group_package_types=mandatory,default,optional
sudo yum groupinstall 'Platform Development'
sudo yum groupinstall 'Python'
sudo yum groups mark install "Virtualization Hypervisor"

#########
sudo dmidecode -t bios  
cat /proc/cpuinfo   
cat /etc/redhat-release 
cat /proc/version   
#########

tar -zxf a10_gx_pac_ias_1_1_prq_rte_installer.tar.gz -C /opt/sysoft/
cd /opt/sysoft/a10_gx_pac_ias_1_1_prq_rte_installer/
mkdir /opt/sysoft/intelrtestack_1.1
./setup.sh

cd ../intelrtestack_1.1/
source init_env.sh

wget -c https://www.intel.com/content/dam/altera-www/global/en_US/others/solutions/acceleration-hub/a10_gx_pac_ias_1_1_pv_eth.patch
cp a10_gx_pac_ias_1_1_pv_eth.patch a10_gx_pac_ias_1_1_pv/hw/
cd a10_gx_pac_ias_1_1_pv/hw/
patch -s -p0 < a10_gx_pac_ias_1_1_pv_eth.patch 

#安装OPAE Framework 
sudo yum install gcc gcc-c++ cmake make autoconf automake libxml2 libxml2-devel json-c-devel boost ncurses ncurses-devel ncurses-libs boost-devel libuuid libuuid-devel python2-jsonschema doxygen hwloc-devel libpng12 rsync
#1 Install the FPGA driver
  a Remove any previous version of the OPAE framework
    sudo yum remove opae*.x86_64
  b Install the Extra Packages for Enterprise Linux (EPEL):
    #sudo yum install epel-release
  c Change to the OPAE installation software directory:
    cd /opt/sysoft/intelrtestack_1.1/a10_gx_pac_ias_1_1_pv/sw/
  d Install the driver:
    sudo yum install opae-intel-fpga*.rpm
#2 Install the latest OPAE framework:
    sudo yum install opae*.rpm
#3 Update dynamic linker run-time bindings:
    sudo ldconfig
#4 Check the Linux kernel installation:
    lsmod | grep fpga

#5 Verify your library installation:
    ls /usr/lib64/libopae-c* -l
#Run the fpgainfo tool to identify the FIM currently loaded
    sudo fpgainfo fme
cd ..
rm -rf a10_gx_pac_ias_1_1_pv_rte_installer/
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WashU_install

pip install SOAPpy
sudo service mysqld start
sudo yum install libpng ghostscript GMT hdf5
sudo yum install zlib-devel ncurses-devel
sudo yum install openssl-devel
sudo yum install openssl-devel
sudo yum install curl-devel
sudo yum install libssh2-devel
sudo yum install librsvg2-devel
tar -xf /home/train/software/libpng-1.2.59.tar.xz -C /home/train/
cd
cd libpng-1.2.59/
mkdir /opt/sysoft/libpng12
./configure --prefix=/opt/sysoft/libpng12/
make -j 8
make install
echo 'export LD_LIBRARY_PATH=/opt/sysoft/libpng12/lib/:$LD_LIBRARY_PATH' >> ~/.bashrc.WashU
echo 'export C_INCLUDE_PATH=/opt/sysoft/libpng12/include/:$C_INCLUDE_PATH' >> ~/.bashrc.WashU
source ~/.bashrc.WashU
sudo vim /etc/httpd/conf/httpd.conf
<IfModule mpm_worker_module>
   LoadModule cgid_module modules/mod_cgid.so
</IfModule>
<IfModule mpm_event_module>
   LoadModule cgid_module modules/mod_cgid.so
</IfModule>
<IfModule mpm_prefork_module>
   LoadModule cgi_module modules/mod_cgi.so
</IfModule>
sudo service httpd start
cd
rm -rf libpng-1.2.59/
mkdir WashU
cd WashU/
git clone https://github.com/epgg/eg.git

#Compile the cgi-bin program
cd eg/cgi-bin/jsmn-example/
sudo vim /etc/httpd/conf/httpd.conf
LoadModule cgid_module modules/mod_cgid.so
Options FollowSymLinks ExecCGI
AddHandler cgi-script .cgi

sudo yum install jsoncpp-devel
scp root@192.168.199.220:/root/Downloads/curl-7.61.1.tar.gz /home/train/software/
tar -zxf /home/train/software/curl-7.61.1.tar.gz -C /home/train/
cd /home/train/curl-7.61.1/
mkdir /opt/sysoft/curl-7.61.1
./configure --prefix=/opt/sysoft/curl-7.61.1/
make -j 8
make test
make install
echo 'export LD_LIBRARY_PATH=/opt/sysoft/curl-7.61.1/lib/:$LD_LIBRARY_PATH' >> ~/.bashrc.WashU
echo 'export C_INCLUDE_PATH=/opt/sysoft/curl-7.61.1/include/:$C_INCLUDE_PATH' >> ~/.bashrc.WashU
echo 'export PATH=/opt/sysoft/curl-7.61.1/bin/:$PATH' >> ~/.bashrc.WashU
source ~/.bashrc.WashU
cd ..
rm -rf curl-7.61.1/
cd /home/train/WashU/eg/cgi-bin/jsmn-example
make
cd ../jsmn/
make 
cd ..
cp subtleKnife.c subtleKnife.c.bak
vim subtleKnife.c
#define WWWT "/var/www/html/browser/t" // Docker version
#define BINdir "."
#define Mysqlserver "localhost" // Deployment version
#define Mysqlserver "localhost" // Docker version
#define Mysqluser "hguser"
#define Mysqlpswd "hguser"
cp postdeposit.c postdeposit.c.bak
vim postdeposit.c
#define WWWT "/var/www/html/browser/t" // Docker version
make 
sudo cp postdeposit subtleKnife /var/www/cgi-bin/
sudo cp ucsc2jsonhub.py /var/www/cgi-bin/

#Directories
sudo mkdir -p /var/www/html/browser/t
sudo mkdir /srv/epgg
sudo chown apache.apache /srv/epgg/
sudo mkdir /srv/epgg/data
cd /srv/epgg/data/
sudo mkdir data
cd data/
sudo mkdir subtleKnife
cd subtleKnife/
sudo mkdir seq
sudo mkdir /srv/epgg/data/data/subtleKnife/hg19
sudo mkdir /srv/epgg/data/data/subtleKnife/hg19/config
sudo mkdir /srv/epgg/data/data/subtleKnife/hg19/session
sudo mkdir /srv/epgg/data/trash
sudo chown apache.apache /srv/epgg/data/trash/
sudo ln -s /srv/epgg/data/trash /usr/lib

cd ~/WashU/eg/
cd browser/
sudo mv css/ index.html js/ images/ /var/www/html/browser/
cd ..
sudo mv config/treeoflife /srv/epgg/data/data/subtleKnife/
sudo cp config/hg19/tracks.json /srv/epgg/data/data/subtleKnife/hg19/config/
sudo cp config/hg19/publichub.json /srv/epgg/data/data/subtleKnife/hg19/config/
cd /srv/epgg/data/data/subtleKnife/hg19/
sudo vim hg19_download.sh
####################################
wget -c http://egg.wustl.edu/d/hg19/refGene.gz
wget -c http://egg.wustl.edu/d/hg19/refGene.gz.tbi
wget -c http://egg.wustl.edu/d/hg19/gencodeV17.gz
wget -c http://egg.wustl.edu/d/hg19/gencodeV17.gz.tbi
wget -c http://egg.wustl.edu/d/hg19/xenoRefGene.gz
wget -c http://egg.wustl.edu/d/hg19/xenoRefGene.gz.tbi
####################################
sudo bash hg19_download.sh
sudo rm hg19_download.sh

mysql -u root -p123456
mysql> GRANT ALL ON *.* TO 'hguser'@'localhost' IDENTIFIED BY 'hguser' WITH GRANT OPTION;
mysql> FLUSH PRIVILEGES;
mysql> CREATE DATABASE hg19;
mysql> FLUSH PRIVILEGES;
mysql> QUIT
cd ~/WashU/eg/config/
cat sessionUtils.sql | mysql -u hguser -p hg19
cd hg19
cat makeDb.sql | mysql -u hguser -p hg19
sudo vim /etc/httpd/conf/httpd.conf
#############################
<Location /var/www/cgi-bin>
Header set Access-Control-Allow-Origin "*"
</Location>
#############################
sudo service httpd restart
sudo service mysqld restart

cd /srv/epgg/data/data/subtleKnife/seq/
sudo wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19.gz http://epgg-test.wustl.edu/installdata/hg19.gz.tbi

cd
mkdir -p ~/WashU/webdata/hg19
cd ~/WashU/webdata/hg19/
vim download.sh
##########################################################
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_ensemble.gz
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_ensemble.gz.tbi
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_all.gz
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk_all.gz.tbi
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/cpgisland.gz
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/cpgisland.gz.tbi

wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/rmsk.tgz

wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/placentalphastCons46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/placentalphastCons46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/placentalphyloP46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/placentalphyloP46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/primatephastCons46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/primatephastCons46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/primatephyloP46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/primatephyloP46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephastCons46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephastCons46way.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephyloP46way.gz \
http://epgg-test.wustl.edu/installdata/hg19/vertebratephyloP46way.gz.tbi

wget -c -b -q http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign100mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign24mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign36mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign40mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign50mer.bigWig \
http://epgg-test.wustl.edu/installdata/hg19/wgEncodeCrgMapabilityAlign75mer.bigWig
##########################################################################################
tar zxvf rmsk.tgz
sudo ln -sv /home/train/WashU/webdata/hg19/* /srv/epgg/data/data/subtleKnife/hg19/
cd /srv/epgg/data/data/subtleKnife/
sudo wget http://epgg-test.wustl.edu/installdata/hg19/sql.tgz
sudo tar -zxf sql.tgz 
sudo rm sql.tgz
cd hg19/
cat load.sql | mysql -u hguser -p hg19
cd ~/WashU/eg/config/hg19/
cat makeDb.sql ../sessionUtils.sql | mysql -u hguser -p hg19

cd /srv/epgg/data/data/subtleKnife/
sudo mkdir hg38
cd hg38/
sudo vim download.sh
#######################################
wget -c -b -q http://epgg-test.wustl.edu/installdata/hg38/gc5Base.bigWig \
http://epgg-test.wustl.edu/installdata/hg38/refGene.gz \
http://epgg-test.wustl.edu/installdata/hg38/refGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/xenoRefGene.gz \
http://epgg-test.wustl.edu/installdata/hg38/xenoRefGene.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_all.gz \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_all.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_ensemble.gz \
http://epgg-test.wustl.edu/installdata/hg38/rmsk_ensemble.gz.tbi \
http://epgg-test.wustl.edu/installdata/hg38/rmsk.gz \
#######################################
cd
cd WashU/webdata/
mkdir hg38
cd hg38
sudo mv /srv/epgg/data/data/subtleKnife/hg38/download.sh /home/train/WashU/webdata/hg38/
bash download.sh
wget -c https://epgg-test.wustl.edu/installdata/hg38/rmsk_ensemble.gz.tbi
wget -c https://epgg-test.wustl.edu/installdata/hg38/rmsk.tgz
tar -zxf rmsk.tgz
cd /srv/epgg/data/data/subtleKnife/hg38/
sudo mkdir config
sudo mkdir session
sudo chown apache.apache /srv/epgg/data/data/subtleKnife/hg38/session/
sudo cp ../hg19/config/publichub.json config/
sudo ln -sv /home/train/WashU/webdata/hg38/* /srv/epgg/data/data/subtleKnife/hg38/
sudo wget http://epgg-test.wustl.edu/installdata/hg38/sql.gz
sudo gunzip sql.gz
sudo mysql -u root -p123456
mysql> CREATE DATABASE hg38;
mysql> FLUSH PRIVILEGES;
mysql> quit
cat sql | mysql -u hguser -p hg38
cd ../seq/
sudo wget -c -b -q http://epgg-test.wustl.edu/installdata/hg38.gz http://epgg-test.wustl.edu/installdata/hg38.gz.tbi

cd
cd software/
wget http://hgdownload.soe.ucsc.edu/admin/jksrc.zip
cp jksrc.zip /home/train/
unzip jksrc.zip -d /opt/sysoft/
cd /opt/sysoft/kent/src/
export MACHTYPE="x86_64"
export USE_SSL=1
sudo yum install uuid-devel.x86_64
sudo yum install uuid-c++-devel.x86_64
sudo yum install libuuid-devel
make libs
mkdir utils/bwquery
cd utils/bwquery/
cp ~/WashU/eg/cgi-bin/bwquery/* .
make 
sudo ln -sv /opt/sysoft/kent/src/utils/bwquery/ /var/www/cgi-bin/
/var/www/cgi-bin/bwquery/bwquery https://vizhub.wustl.edu/hubSample/hg19/sample.bigWig chr7 27053199 27373567 20 /opt/sysoft/kent/src/utils/bwquery/bwOutput.txt 1
sudo cp bwOutput.txt /srv/epgg/data/data/subtleKnife/hg19/

cd /srv/epgg/data
sudo tar -xf /home/train/software/samtools-0.1.19.tar.bz2 -C /srv/epgg/data/
cd samtools-0.1.19/
sudo make 
sudo ln -sv /srv/epgg/data/samtools-0.1.19/samtools /usr/local/bin/
cd /opt/sysoft/
mkdir -p subtleKnife/scripts/bamliquidator
cd subtleKnife/scripts/bamliquidator/
wget -c https://egg.wustl.edu/script/bamliquidator/bamliquidator.c
wget https://egg.wustl.edu/script/bamliquidator/bamliquidator.o
wget https://egg.wustl.edu/script/bamliquidator/make.sh
chmod 755 make.sh 
sudo ./make.sh 
cp bamliquidator /usr/local/bin/
sudo yum install sendmail-devel

cd /srv/epgg/data/
sudo tar -xf /home/train/software/tabix-0.2.6.tar.bz2 -C /srv/epgg/data/
cd tabix-0.2.6/
sudo make 
sudo ln -sv /srv/epgg/data/tabix-0.2.6/tabix /usr/local/bin/
发表在 3D_genome_browser | 留下评论

Rosetta_install

source ~/.bashrc.gcc-4.9.3
mkdir /opt/sysoft/llvm_clang-3.4.2
cd /home/train/data/software/Clang
tar -zxf cfe-3.4.2.src.tar.gz
tar -zxf clang-tools-extra-3.4.src.tar.gz
tar -zxf compiler-rt-3.4.src.tar.gz
tar -zxf dragonegg-3.4.src.tar.gz
tar -zxf libcxx-3.4.2.src.tar.gz
tar -zxf lld-3.4.src.tar.gz
tar -zxf lldb-3.4.src.tar.gz
tar -zxf llvm-3.4.2.src.tar.gz
tar -zxf polly-3.4.src.tar.gz
tar -zxf test-suite-3.4.src.tar.gz
mkdir LLVM_3.4.2
mv *.gz LLVM_3.4.2
mv llvm-3.4.2.src/ llvm
mv cfe-3.4.2.src/ clang
mv clang/ llvm/tools/
mv clang-tools-extra-3.4/ extra
mv extra/ llvm/tools/clang/tools/
mv compiler-rt-3.4/ compiler-rt
mv compiler-rt/ llvm/projects/
mv lld-3.4/ lld
mv lld llvm/tools/
mv polly-3.4/ polly
#mv polly/ llvm/tools/
mv libcxx-3.4.2.src/ libcxx
mv libcxx/ llvm/projects/
mv test-suite-3.4/ test-suite
mv test-suite/ llvm/projects/
mv lldb-3.4/ lldb
#mv lldb/ llvm/tools/
mv dragonegg-3.4/ dragonegg
mkdir build
cd build/
../llvm/configure --prefix=/opt/sysoft/llvm_clang-3.4.2/ --enable-optimized --enable-assertions --enable-targets=host-only
#若出现isl required but not found,则说明需要安装isl
wget -c http://isl.gforge.inria.fr/isl-0.13.tar.gz
tar -zxf isl-0.13.tar.gz
cd isl-0.13
mkdir /opt/sysoft/isl-0.13
./configure --prefix=/opt/sysoft/isl-0.13/
make -j 8 && make install
sudo ln -sv /opt/sysoft/isl-0.13/include/isl /usr/include/isl-0.13
../llvm/configure --prefix=/opt/sysoft/llvm_clang-3.4.2/ --enable-optimized --enable-assertions --enable-targets=host-only --with-isl=/opt/sysoft/isl-0.13/ --with-cuda=/usr/local/cuda-9.2/
#若出现unrecognized options: --enable-optimized, --enable-assertions, --enable-targets,因为不可以将polly文件夹先放入llvm的tools文件夹下
#../llvm/configure --prefix=/opt/sysoft/llvm_clang-3.4.2/ --with-isl=/opt/sysoft/isl-0.13/ --with-cuda=/usr/local/cuda-9.2/
make -j 10
make check-all
make install
sudo vim /etc/ld.so.conf.d/llvm_clang-3-4-2.conf
#写入如下
/opt/sysoft/llvm_clang-3.4.2/lib/
sudo ldconfig
sudo ln -sv /opt/sysoft/llvm_clang-3.4.2/include/* /usr/include/
sudo ln -sv /opt/sysoft/llvm_clang-3.4.2/include/c++ /usr/include/llvm-clang-c++
echo 'PATH=$PATH:/opt/sysoft/llvm_clang-3.4.2/bin/' >> ~/.bashrc
source ~/.bashrc
source ~/.bashrc.gcc-4.9.3
clang --version
rm -rf build/ llvm/

tar -zxf scons-3.0.1.tar.gz
mkdir /opt/sysoft/SCons-3.0.1
python setup.py install --prefix=/opt/sysoft/SCons-3.0.1/
ln -sv /opt/sysoft/SCons-3.0.1/lib/scons-3.0.1/SCons /opt/sysoft/Python-2.7.11/lib/python2.7/site-packages/
echo 'PATH=$PATH:/opt/sysoft/SCons-3.0.1/bin/' >> ~/.bashrc
source ~/.bashrc
cd ..
rm -rf scons-3.0.1
mkdir /opt/biosoft/rosetta-3.9
tar -zxf rosetta_src_3.9_bundle.tgz -C /opt/biosoft/rosetta-3.9
cd /opt/biosoft/rosetta-3.9/rosetta_src_2018.09.60072_bundle/
cd main/source/
export PATH=/usr/lib64/openmpi/bin/:$PATH
./scons.py -j 20 bin mode=release extras=mpi
echo 'PATH=$PATH:/opt/biosoft/rosetta-3.9/rosetta_src_2018.09.60072_bundle/main/source/bin/' >> ~/.bashrc
source ~/.bashrc

mkdir /opt/biosoft/PyRosetta4-python27
tar -xf PyRosetta4.Release.python27.linux.release-189.tar.bz2 -C /opt/biosoft/PyRosetta4-python27/
cd /opt/biosoft/PyRosetta4-python27/PyRosetta4.Release.python27.linux.release-189/
cd setup/
source ~/.bashrc_local_python_2.7
python setup.py install
#不可以设置路径,最终安装到的路径为
#/opt/sysoft/Python-2.7.11/lib/python2.7/site-packages/pyrosetta-2018.34+release.14e0a7a-py2.7-linux-x86_64.egg/
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Ubuntu16固定IP的修复

lshw -C network #查看网卡的信息   
#ifconfig enp15s0 固定ip netmask 255.255.255.0 #临时固定ipi地址
/etc/init.d/networking stop
cp /etc/network/interfaces /etc/network/interfaces.bak
### enp15s0和enp14s0是一个网卡的两个接口
vim /etc/network/interfaces
#添加如下    
auto enp15s0
auto enp14s0
iface enp14s0 inet dhcp   #动态ip
iface enp15s0 inet static #固定ip
address 固定ip地址
netmask 255.255.255.0

vim /etc/hosts
固定ip地址    bioinf.njnu.edu.cn

vim /etc/resolv.conf #设置DNS解析---个人觉得可以不用 
nameserver 固定ip地址

ifconfig enp14s0 up
dhclient enp14s0     
ifconfig enp15s0 up
/etc/init.d/networking start


注意:因为这里的enp14s0是可以链接外网的接口,所以需要先将电脑链接到外网,然后启动enp15s0是将网卡的另一个接口绑定固定ip,由于并未设定链接规则,所以外网可以直接访问此固定ip,若需要制定访问规则可以自己根据规则定义
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GROMACS-2018.3安装(Intel编译器+GPU)

#The GROMACS team recommends OpenMPI version 1.6 (or higher), MPICH version 1.4.1 (or higher), or your hardware vendor's MPI installation.
#说明gromacs支持intel cpu 的mpi加速,因此先确定是否安装 intel_Parallel_Studio_XE
tar -zxf gromacs-2018.3.tar.gz -C /opt/biosoft/
cd /opt/biosoft/gromacs-2018.3/
#Check that you have CMake version 3.4.3 or later
cmake --version
#cmake version 3.4.3
mkdir build
cd build/
source /opt/intel/compilers_and_libraries_2017.7.259/linux/bin/compilervars.sh intel64
export PATH=/opt/sysoft/gcc-4.9.3/bin/:$PATH
export LD_LIBRARY_PATH=/opt/sysoft/gcc-4.9.3/lib/:$LD_LIBRARY_PATH  
export LD_LIBRARY_PATH=/opt/sysoft/gcc-4.9.3/lib64/:$LD_LIBRARY_PATH 
export C_INCLUDE_PATH=/opt/sysoft/gcc-4.9.3/include/:$C_INCLUDE_PATH 
export CPLUS_INCLUDE_PATH=/opt/sysoft/gcc-4.9.3/include/:$CPLUS_INCLUDE_PATH 
cmake .. -DGMX_FFT_LIBRARY=mkl -DCMAKE_C_COMPILER=/opt/intel/bin/icc -DCMAKE_CXX_COMPILER=/opt/intel/bin/icc -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.2/ -DCUDA_HOST_COMPILER=/opt/intel/bin/icc -DGMX_SIMD=AVX_256 -DREGRESSIONTEST_PATH=/home/train/data/software/Gromacs5.07/regressiontests-5.0.7/  -DCMAKE_INSTALL_PREFIX=/opt/biosoft/gromacs2018_3/ 
make 
make check
#若出现如下:
#Failing SIMD math function ulp comparison between std::exp and expSingleAccuracy<MathOptimization::Unsafe>
#Requested ulp tolerance: 16
#Requested abs tolerance: 0
#Denormals can be 0: false
#Largest Ulp difference occurs for x=-86.983924865722656
#Ref  values: 1.6724818069065022e-38
#SIMD values: 2.350988701644575e-38
#Ulp diff.:   4841987
#仅仅是用intel编译器算出来的值和gcc编译器算出来的值略有不同,不放心可以重新编译intel 编译器,再进行重新编译gromacs
make install

#mdrun_only_intel编译器重新编译
source /opt/intel/compilers_and_libraries_2017.7.259/linux/bin/compilervars.sh intel64
mkdir /opt/biosoft/gromacs_mdrunonly_2018_3
cd /opt/biosoft/gromacs-2018.3
mkdir build-normal
cd build-normal/
export PATH=/opt/sysoft/Python-2.7.11/bin/:$PATH
cmake .. -DGMX_FFT_LIBRARY=mkl -DCMAKE_C_COMPILER=/opt/intel/bin/icc -DCMAKE_CXX_COMPILER=/opt/intel/bin/icc -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.2/ -DCUDA_HOST_COMPILER=/opt/intel/bin/icc -DGMX_SIMD=AVX_256 -DCMAKE_INSTALL_PREFIX=/opt/biosoft/gromacs_mdrunonly_2018_3/ 
make 
make install
cd ..
mkdir build-mdrun-only
cd build-mdrun-only/
cmake .. -DGMX_FFT_LIBRARY=mkl -DCMAKE_C_COMPILER=/opt/intel/bin/icc -DCMAKE_CXX_COMPILER=/opt/intel/bin/icc -DMKL_LIBRARIES=/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/ -DMKL_INCLUDE_DIR=/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/include/ -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.2/ -DCUDA_HOST_COMPILER=/opt/intel/bin/icc -DGMX_SIMD=AVX_256 -DGMX_BUILD_MDRUN_ONLY=ON -DCMAKE_INSTALL_PREFIX=/opt/biosoft/gromacs_mdrunonly_2018_3/ 
make
make install
cd /home/train/data/software/Gromacs5.07/regressiontests-5.0.7
source /opt/biosoft/gromacs_mdrunonly_2018_3/bin/GMXRC
./gmxtest.pl all -np 2#若显示
#Index  Reference   This test       Error  Description
#   5    -2521.58    -2400.27   0.0246464  1aml.pdb with oplsaa using vsite=none and water=tip3p
#   6    -2521.58    -2400.27   0.0246464  1aml.pdb with oplsaa using vsite=none and water=tip4p
#   7    -2521.58    -2400.27   0.0246464  1aml.pdb with oplsaa using vsite=none and water=tip5p
#   8    -2265.25    -2126.91   0.0314959  1aml.pdb with oplsaa using vsite=h and water=tip3p
#   9    -2265.25    -2126.91   0.0314959  1aml.pdb with oplsaa using vsite=h and water=tip4p
#  10    -2265.25    -2126.91   0.0314959  1aml.pdb with oplsaa using vsite=h and water=tip5p
#   There were 6/42 differences in final energy with the reference file
#   pdb2gmx tests FAILED
#提示计算误差,不必担心是由于计算机本身的硬件决定
echo 'PATH=$PATH:/opt/biosoft/gromacs_mdrunonly_2018_3/bin/' >> ~/.bashrc
source ~/.bashrc
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