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README
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# RNAHeliCes and HiKinetics
Abstract folding space analysis based on helices and RNA-kinetics based on folding space abstraction
Copyright (C) 2011-20 Jiabin Huang, Björn Voss.
Send comments/bug reports to: J. Huang <j.huang@uke.de>.
## Dependencies
(Optional) if without SUPER privilege, install libboost locally
#install boost without root access
#https://programmer.ink/think/how-to-compile-and-install-boost-libraries-on-linux.html
#under conda-env cc_env # gcc5.4
#NEED python2.7: downgrade the python from 3.8 --> 2.7
```sh
conda create --name gcc6 python=2.7
conda activate gcc6
conda install gxx_linux-64
conda deactivate
conda create --name gcc5 --clone gcc6
conda remove --name gcc6 --all
conda activate gcc5
#TODO: install cc_env as hamm
conda install python=2.7
./bootstrap.sh --with-libraries=all /your_path/anaconda3/envs/cc_env/bin/x86_64-conda_cos6-linux-gnu-gcc
#./bootstrap.sh --with-libraries=date_time,program_options --with-toolset=gcc
#./bootstrap.sh --with-libraries=all --with-toolset=gcc
#https://www.ibm.com/developerworks/library/i-building-boost-libraries-using-xlcpp-toolset-trs/index.html
#./b2 install cxxflags="-qnoxlcompatmacros" cflags="-qnoxlcompatmacros" --prefix=$BOOST_ INSTALL --build-dir=$BOOST_BUILD -j8 -l1200 toolset=xlcpp variant=release target-os=linux -s OS=LINUX -d2 -a
./b2 install cxxflags="-std=c++98" -j12 --prefix=/home/jhuang/Tools/boost_1_58_installed
#./b2 install --prefix=/your_path/boost_1_58_installed #--with-toolset=/your_path/anaconda3/envs/cc_env/bin/gcc
#ldconfig # requires the root permission!
```
## Installation
```sh
git clone https://github.com/huang/RNAHeliCes
./configure CFLAGS="-fno-stack-protector" CPPFLAGS="-std=c++98" CXXFLAGS="-std=c++98 -fno-stack-protector"
make
sudo make install
```
Notes:
- If there are any linking problems after installing, please check if /usr/local/lib is contained in the environmental variable LD_LIBRARY_PATH.
- ./src/libs/libRNA.a contains all Vienna package routines, this may be system dependent. If so, please reload this from Vienna RNA Package.
- If without SUPER privilege, use
./configure --with-boost-include-path="/your_path/boost_1_58_installed/include" --with-boost-lib-path="/your_path/boost_1_58_installed/lib" CFLAGS='-g -O2 -fno-stack-protector' CPPFLAGS='-std=c++98 -I/your_path/boost_1_58_installed/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2' CXXFLAGS='-std=c++98 -g -O2 -w -fno-stack-protector'
## Test run
```sh
RNAHeliCes examples/collosoma_slrna.seq #abstract folding space analysis based on helices
HiPath -f examples/switches_4.faa -k 40 -P ./librna/vienna/rna_turner1999.par #calculating energy barriers of an energy landscape
HiTed examples/riboswitches.fas -t 1 -r 1 #calculating minimum Hishape based Tree edit distance
```
## HiKinetics
See ./HiKinetics/README for HiKinetics.
## INSTALL and COPYING
See "INSTALL" for detailed installation instructions, and
"COPYING" for disclaimer and copyright.
## Citations
[1] Huang, J., & Voß, B. (2011, September). RNAHeliCes—Folding Space Analysis Based on Position Aware Structure Abstraction. In German Conference on Bioinformatics, Weihenstephan, Germany (Vol. 79).
[2] Huang, J., Backofen, R., & Voß, B. (2012). Abstract folding space analysis based on helices. RNA, 18(12), 2135-2147.
[3] Huang, J., & Voß, B. (2012, September). Reducing the search space in RNA helix based folding. European Conference on Computational Biology 2012. European Conference on Computational Biology (ECCB) 2012.
[4] Huang, J., & Voß, B. (2014). Analysing RNA-kinetics based on folding space abstraction. BMC bioinformatics, 15(1), 60.
#---------------------------------------------------------------------
#RNAHeliCes
Copyright (C) 2011-20 Jiabin Huang, Björn Voss.
Send comments/bug reports to: J. Huang <j.huang@uke.de>.
## Dependencies
1. (Optional) if without SUPER privilege, install libboost locally
#install boost without root access
#https://programmer.ink/think/how-to-compile-and-install-boost-libraries-on-linux.html
#under conda-env cc_env # gcc5.4
#NEED python2.7: downgrade the python from 3.8 --> 2.7
conda install python=2.7
./bootstrap.sh --with-libraries=all /home/jhuang/anaconda3/envs/cc_env/bin/x86_64-conda_cos6-linux-gnu-gcc
#./bootstrap.sh --with-libraries=date_time,program_options --with-toolset=gcc
./b2 install --prefix=/home/jhuang/boost_1_58_installed #--with-toolset=/home/jhuang/anaconda3/envs/cc_env/bin/gcc
#ldconfig # requires the root permission!
## Installation
```sh
git clone https://github.com/huang/RNAHeliCes
./configure CFLAGS="-fno-stack-protector" CPPFLAGS="-std=c++98" CXXFLAGS="-std=c++98 -fno-stack-protector"
make
sudo make install
```
Notes:
- If there are any linking problems after installing, please check if /usr/local/lib is contained in the environmental variable LD_LIBRARY_PATH.
- ./src/libs/libRNA.a contains all Vienna package routines, this may be system dependent. If so, please reload this from Vienna RNA Package.
- If without SUPER privilege, use
./configure --with-boost-include-path="/home/jhuang/boost_1_58_installed/include" --with-boost-lib-path="/home/jhuang/boost_1_58_installed/lib" CFLAGS='-g -O2 -fno-stack-protector' CPPFLAGS='-std=c++98 -I/home/jhuang/boost_1_58_installed/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2' CXXFLAGS='-std=c++98 -g -O2 -w -fno-stack-protector'
## Test run
```sh
RNAHeliCes examples/collosoma_slrna.seq' #run an example
HiPath -h #get help for calculating energy barriers of an energy landscape
HiPath -f examples/switches_4.faa -k 40 -P ./librna/vienna/rna_turner1999.par #run an example
HiTed -h #get help for calculating minimum Hishape based Tree edit distance
HiTed examples/riboswitches.fas -t 1 -r 1 #run an example.
```
## HiKinetics
See ./HiKinetics/README for HiKinetics.
## INSTALL and COPYING
See "INSTALL" for detailed installation instructions, and
"COPYING" for disclaimer and copyright.
## Citations
[1] Huang, J., & Voß, B. (2011, September). RNAHeliCes—Folding Space Analysis Based on Position Aware Structure Abstraction. In German Conference on Bioinformatics, Weihenstephan, Germany (Vol. 79).
[2] Huang, J., Backofen, R., & Voß, B. (2012). Abstract folding space analysis based on helices. RNA, 18(12), 2135-2147.
[3] Huang, J., & Voß, B. (2014). Analysing RNA-kinetics based on folding space abstraction. BMC bioinformatics, 15(1), 60.