CentOS 7 comes with gcc 4.8.5 but MrTrix needs 4.9+, also it needs Qt-qtsvg To do this, addition to the mrtrix install instruction: yum install qt5-qtsvg qt5-qtsvg-devel qt5-qtbase-devel devtoolset-3-gcc.x86_64 devtoolset-3-gcc-c++.x86_64 export QTDIR=/usr/lib64/qt5;export PATH=/usr/lib64/qt5/bin/:$PATH; export CXX=/opt/rh/devtoolset-3/root/usr/bin/g++; ./configure ./build Then you get it.
Enable OpenGL forwarding in cygwin and linux
In cygwin, if you start X server using command: $ X -multiwindow -nowgl +iglx & and $ export LIBGL_ALWAYS_INDIRECT=1 $ export DISPLAY=:0.0 you will have a GLX functionality over ssh through indirect software rendering if you start X server using command: $ X -multiwindow -wgl +iglx & and $ export LIBGL_ALWAYS_INDIRECT=1 $ export DISPLAY=:0.0 you […]
LDAPS authentication for GALAXY when you use self-signed certificate
The current version of GALAXY (https://usegalaxy.org/) will run into error when using ldaps authentication mechanics. The error is Traceback (most recent call last): File “/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py”, line 117, in authenticate ldap.set_option(_opt) File “/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/ldap/functions.py”, line 135, in set_option return _ldap_function_call(None,_ldap.set_option,option,invalue) File “/home/galaxy/galaxy-dist/.venv/local/lib/python2.7/site-packages/ldap/functions.py”, line 66, in _ldap_function_call result = func(_args,**kwargs) ValueError: option error The function in Python LDAP […]
Installing Melview on CentOS7
git clone http://users.fmrib.ox.ac.uk/~flitney/melview.git wget ftp://ftp.pbone.net/mirror/archive.fedoraproject.org/fedora-secondary/releases/14/Everything/arm/os/Packages/python-EnthoughtBase-3.0.5-1.fc14.noarch.rpm yum install python-EnthoughtBase-3.0.5-1.fc14.noarch.rpm yum install python-matplotlib-qt4 python-matplotlib python-pyside python-configobj pip install -U pip pip install -U traits traitsui nibabel pyface cd melview python ./setup.py install
Linux create salted password
Method 1 openssl passwd -1 -salt xyz yourpass Method 2 makepasswd –clearfrom=- –crypt-md5 <<< YourPass Method 3 echo "username:password" | chpasswd Or you can use encrypted password with chpasswd first generate it using : perl -e 'print crypt("YourPasswd", "salt"),"\n"' then later you can use generated password to update echo "username:encryptedPassWd" | chpasswd -e this encrypted […]
Yum is not compatible with Matlab Runtime
So do not put matlab runtime into ld.so.conf.d. If yum broken, remove that file and do ldconfig.
du only local files
sudo find . -maxdepth 1 -type d ! -name . -exec du -sh ‘{}’ \; | sort -h
Matlab: libGL error: dlopen /usr/lib64/dri/swrast_dri.so failed
Starting Matlab R2015a or newer in CentOS7 or recent version of Fedora, the error libGL error: dlopen /usr/lib64/dri/swrast_dri.so failed will rise through does not affect the normal working of Matlab. This problem is caused by the libstdc++.so.6 coming with Matlab. Matlab carries statically linked libstdc++.so.6.0.17 in /matlab_folder/sys/os/glnxa64. When the system version of libstdc++.so.6 is lower […]
htdigest
htdigest [-c for create password file] password_file_name ‘realm name’ username it will prompt you twice for a password.
qap installation
pip install –upgrade numpy scipy && pip install –upgrade nipype nibabel nitime pyyaml pandas cd qap python setup.py install