在Centos6.5上对gdc-client进行源码安装

  source ~/.bashrc_python-2.7.11 #事先安装好Python2.7以上的版本
  git clone git@github.com:NCI-GDC/gdc-client.git
  vim requirements.txt
          -e /home/train/gdc-tool/parcel #指定本地安装parcel,不然因为外网,无法下载
  pip install -r requirements.txt
  pip install -r dev-requirements.txt
  python setup.py install
  python -m pytest --cov=gdc_client --cov-branch --cov-report term tests/

  echo 'PATH=$PATH:/home/train/gdc-tool/gdc-client/bin' >> ~/.bashrc
  source ~/.bashrc

  #如果遇到'DownloadStream' object has no attribute 'url'的问题
  cd /home/train/gdc-tool/gdc-client/gdc_client/download
  cp client.py client.py.bak
  # gdc-client calls parcel's parallel_download,
  # which is where most of the downloading takes place
      file_id = stream.uri.split('/')[-1] # l -> i

  cd /home/train/gdc-tool/gdc-client
  python setup.py install
  rm -rf /home/train/gdc-tool/gdc-client/gdc_client/
发表在 TCGA | 留下评论

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
  • Oncomine —-> compute gene expression signatures, clusters and
    gene-set modules, automatically extracting biological insights from
    the data
  • LinkedOmics —-> The web application has three analytical modules:
    LinkFinder, LinkInterpreter and LinkCompare. LinkFinder allows users
    to search for attributes that are associated with a query attribute,
    such as mRNA or protein expression signatures of genomic alterations,
    candidate biomarkers of clinical attributes, and candidate target
    genes of transcriptional factors, microRNAs, or protein kinases.
    Analysis results can be visualized by scatter plots, box plots, or
    Kaplan-Meier plots. To derive biological insights from the
    association results, the LinkInterpreter module performs enrichment
    analysis based on Gene Ontology, biological pathways, network
    modules, among other functional categories. The LinkCompare module
    uses visualization functions (interactive venn diagram, scatter plot,
    and sortable heat map) and meta-analysis to compare and integrate
    association results generated by the LinkFinder module, which
    supports multi-omics analysis in a cancer type or pan-cancer
    analysis.
  • GeneMANIA —-> predict the function of your favorite genes and
    gene sets
发表在 TCGA | 留下评论

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")
发表在 R | 留下评论

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

发表在 实验操作 | 留下评论

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!
发表在 TCGA | 留下评论

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)

发表在 Linux | 留下评论

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/
发表在 Linux | 留下评论

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/
发表在 Molecular Dynamics | 留下评论

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
发表在 Linux | 留下评论