I am trying to install Bioperl package in Perl environment of version 5.20.0,
But I am unable to get in to the stuffs.
Idea and suggestion of websites varies and its going to be uneasy for me.
Please suggest me the protocols for installing Bioperl in Ubuntu 12.04LS.
Source: http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server
Install and Configure a Basic Ubuntu Server
Do install then configure.
apt-get clean
apt-get update
apt-get upgrade
apt-get install ssh screen
apt-get clean
Install as much as possible with apt-get
Enable Universe and Multiverse in /etc/apt/sources.list
apt-get update
apt-get install \
lynx unzip zip ncftp gcc libc6-dev make mysql-server apache2 \
perl libgd-gd2-perl libcgi-session-perl libclass-base-perl libexpat1-dev
apt-get clean
Install CPAN and perl modules not available via apt-get
cpan -i 'Text::Shellwords' # choose defaults if first time
Install BioPerl
cd /tmp
wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2
tar -xjvf current_core_unstable.tar.bz2
cd bioperl-*
perl Build.PL # choose the defaults
./Build test
./Build install
Related
I am trying to install snapd but giving this error.
Operating System - Red Hat Enterprise Linux release 8.6 (Ootpa)
Error:
Problem: package snapd-2.57.6-2.el8.x86_64 requires snapd-selinux = 2.57.6-2.el8, but none of the providers can be installed
- conflicting requests
- nothing provides selinux-policy >= 3.14.3-108.el8 needed by snapd-selinux-2.57.6-2.el8.noarch
- nothing provides selinux-policy-base >= 3.14.3-108.el8 needed by snapd-selinux-2.57.6-2.el8.noarch
(try to add '--skip-broken' to skip uninstallable packages or '--nobest' to use not only best candidate packages)
I have the same problem. There's a long discussion about this here: https://forum.snapcraft.io/t/trouble-installing-snapd-on-rhel-8/13140/2. It looks like the only way to do it, if you can install all the necessary build tools, is to build from sources, as one of the posts there suggests.(I couldn't do it on my system because it's having subscription management issues.)
I also tried using CR repository, as suggested in the instructions for CentOS here: https://snapcraft.io/docs/installing-snap-on-centos, but that didn't work for me, either (I guess it's really just for CentOS and not RHEL).
UPDATE:
I finally found a solution (where there's a will...)! I manually installed all the requirements, one by one, that weren't available in the epel-release repo. My process was the following:
wget https://rpmfind.net/linux/centos/8-stream/BaseOS/x86_64/os/Packages/rpm-4.14.3-19.el8.x86_64.rpm
wget https://rpmfind.net/linux/centos/8-stream/BaseOS/x86_64/os/Packages/rpm-libs-4.14.3-19.el8.x86_64.rpm
wget https://dl.rockylinux.org/pub/rocky/8/BaseOS/aarch64/os/Packages/s/selinux-policy-3.14.3-108.el8.noarch.rpm
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/libsemanage-2.9-9.el8.x86_64.rpm --allowerasing -y
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/policycoreutils-2.9-19.el8.x86_64.rpm -y
sudo rpm -i --force rpm-4.14.3-19.el8.x86_64.rpm
sudo rpm -i --force rpm-libs-4.14.3-19.el8.x86_64.rpm
sudo rpm -i --force selinux-policy-3.14.3-108.el8.noarch.rpm
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/python3-libsemanage-2.9-9.el8.x86_64.rpm -y
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/python3-policycoreutils-2.9-19.el8.noarch.rpm -y
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/policycoreutils-python-utils-2.9-19.el8.noarch.rpm -y
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/selinux-policy-minimum-3.14.3-108.el8.noarch.rpm -y
sudo yum install http://mirror.centos.org/centos/8-stream/BaseOS/x86_64/os/Packages/libseccomp-2.5.2-1.el8.x86_64.rpm -y
sudo yum install https://download-ib01.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/s/snapd-selinux-2.57.6-2.el8.noarch.rpm -y
sudo yum install snapd -y
sudo yum update snapd -y
It's conceivable that on your system something else will be missing. If you run into an error telling you that nothing provides package XYZ, you can find it here: https://centos.pkgs.org/8-stream/centos-baseos-x86_64/ and simply sudo yum install directly from the binary package URL; e.g.:
That's exactly what my process was, and here's what I have now:
$ cat /etc/redhat-release (base)
Red Hat Enterprise Linux release 8.2 (Ootpa)
$ snap --version (base)
snap 2.57.6-2.el8
snapd 2.52.1
series 16
rhel 8.2
kernel 4.18.0-193.6.3.el8_2.x86_64
I use command:
cpanm --sudo --interactive Filter::Crypto
I am always asked for location of openssl.
Then I run command:
dpkg -L openssl
I get many paths.
I dont know what should I do next.
thanks
To install this module, the develop files of openssl are needed. Under Ubuntu, it needs to install package: libssl-dev to get develop files to be installed: so after running sudo apt-get install libssl-dev, the problem is resolved.
In CentOS, install openssl-devel package.
I see form my project document that I need to install python-pybind11 by using
sudo apt -y install python-pybind11
but I got error like this:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package python-pybind11
I'm not sure if python-pybind11 is a valid package, where can I check it?
Use this to install pybind11:
pip install pybind11
Refer from Here.
In Ubuntu 18.04
apt-get install python-pybind11
On Mac,
brew install pybind11
In Ubuntu 16.04, you'll need to install yourself. One way is as follows:
# Some prerequisites (but not all of them)
apt-get install cmake
pip3 install pytest
# Clone, build and install
git clone https://github.com/pybind/pybind11.git
cd pybind11
mkdir build
cd build
cmake ..
make install
Reference
In some systems, you may need
sudo apt -y install python3-pybind11
I would like to use Kivy on Eclipse Indigo on Ubuntu 10.04. I understand that python 2.7 is required (2.6 is the default on 10.04) and have python 2.7 installed as well. I've done lots of research but not found an answer. Can I do this and if so how? I don't want to upgrade ubuntu nor Eclipse since this would probably destabilise existing developments.
Kivy and Eclipse are not related, and Eclipse is not necessary for running or editing Kivy programs. I can help to answer the Kivy part of your question, and will leave Eclipse to others.
Since Ubuntu 10.04 is out of support, it's hard to tell which required system packages are not available. This will probably be the most tedious part of the process. For Kivy on Ubuntu 12.04 you need:
sudo apt-get install -y build-essential mercurial git python2.7 python-dev ccache ffmpeg libsdl-image1.2-dev libsdl-mixer1.2-dev libsdl-ttf2.0-dev libsmpeg-dev libsdl1.2-dev libportmidi-dev libswscale-dev libavformat-dev libavcodec-dev zlib1g-dev unzip
Some of those packages will have different versions on Ubuntu 10.04. Hopefully they are all available in some form.
Next you need to bootstrap an up-to-date Python setuptools environment:
sudo apt-get remove --purge -y python-virtualenv python-pip python-setuptools
wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py -O - | sudo python2.7
rm -f setuptools*.zip
sudo easy_install-2.7 -U pip
Now you can install an up-to-date Cython:
sudo apt-get remove --purge -y cython
sudo pip2.7 install -U cython
Next you can install an up-to-date NumPy, which is required for PyGame:
sudo apt-get remove --purge -y python-numpy
sudo pip2.7 install -U numpy
Now you can install an up-to-date PyGame:
sudo apt-get remove --purge -y python-pygame
hg clone https://bitbucket.org/pygame/pygame
cd pygame
python2.7 setup.py build
sudo python2.7 setup.py install
cd ..
sudo rm -rf pygame
Now that all of the dependencies are met, you can install an up-to-date Kivy:
sudo apt-get remove --purge -y python-kivy
sudo pip install -U kivy
In Centos 6.4,when configure Emacs,it shows:
configure: error: The required function `tputs' was not found in any library.
The following libraries were tried (in order):
libtinfo, libncurses, libterminfo, libtermcap, libcurses
Please try installing whichever of these libraries is most appropriate
for your system, together with its header files.
For example, a libncurses-dev(el) or similar package.
How to fix it,what's the problem in it.
sudo yum install ncurses-devel
then ./configure again
Try to install libncurses-dev with
bash
apt-get install libncurses-dev
I'm on a Debian Wheezy derived distribution (CrunchBang)
Trying to install Emacs 24.5.1
Had to install libncurses5-dev, then run ./configure
$ sudo apt-get install ncurses-devel
...
E: Unable to locate package ncurses-devel
$ sudo apt-get install libncurses5-dev