I need some help to install the ABySS assembler on PuTTY (virtual Linux) without root permission (as it takes a long time going via IT department etc.).
To be honest I've no idea where to start from, so I'll be very appreciated for step-by-step guide if that is not too much to ask.
Thanks in advance.
If you are referring to the software here, then it should be sufficient to follow the instructions here. Specifically, you should take note of the part labelled To install ABySS in a specified directory:, and specify a directory in your home directory that you have write access to. For example, I might:
mkdir ~/abyss
./configure --prefix=$HOME/abyss
make
make install
Note that I have removed sudo from before make install, so that you are trying to run the installation as a user rather than root. make install will put the software wherever you specified with --prefix.
However, this all depends upon the source code for any libraries upon which ABySS depends existing on your system as well. I expect you will fail at the ./configure step because some library is missing. In this case download the source code for those libraries and tell configure where you have put them (in your home directory), following the example given for Boost on that same page.
Related
So some background, I'm installing Node on a host server, but it's a grid server not a server that's solely for my website.
The grid server doesn't have a root user/ administrative powers. So to install node I found this workaround: http://iantearle.com/blog/media-temple-grid-and-nodejs . It's a Linux Grid server, I've never used Linux so if someone could explain to me what the commands mean, especially: ./configure --prefix=~/opt/
Lastly I followed the steps but when I try to run the node command in the server it says node:command not found - which is why I'm trying to understand the steps. Thanks
To explain the process:
Configure
The configure script is responsible for getting ready to build the software on your specific system. It makes sure all of the dependencies for the rest of the build and install process are available, and finds out whatever it needs to know to use those dependencies.
Unix programs are often written in C, so we’ll usually need a C compiler to build them. In these cases the configure script will establish that your system does indeed have a C compiler, and find out what it’s called and where to find it.
Make
Once configure has done its job, we can invoke make to build the software. This runs a series of tasks defined in a Makefile to build the finished program from its source code.
The tarball you download usually doesn’t include a finished Makefile. Instead it comes with a template called Makefile.in and the configure script produces a customised Makefile specific to your system.
3.Make Install
Now that the software is built and ready to run, the files can be copied to their final destinations. The make install command will copy the built program, and its libraries and documentation, to the correct locations.
--prefix=~/opt/ -> will set the build directory to /home/yourhome/opt directory.
Now if you didnt get errors while doing those 3 steps explained above make sure you did the following:
nano ~/.bash_profile
export PATH=~/opt/bin:${PATH}
nano is a text editor and you are opening .bash_profile file with it.
you need to add export PATH=~/opt/bin:${PATH} in that file and save it using ctrl+x
Then restart your terminal.
Specified github repository for nodejs is outdated. use the following link instead.
git clone https://github.com/nodejs/node.git
P.S node:command not found usually happens when the program is not installed correctly or it's executable isnt in your terminal's PATH variable.
I'm writing a program that requires LLVM, and thinking of using autotools to ship it on Linux, so from the user's viewpoint the process would look like the well-known ./configure && make && sudo make install.
With autotools, one normally relies on the system package manager to install dependencies. The problem is that, for whatever reason, this doesn't work with LLVM; on Ubuntu 14.04, apt-get thinks the latest version is 3.4, whereas a more recent version would actually be needed. Thus, I need to supply a script to download and build LLVM first (a local copy thereof, not interfering with any older version that might be on the system), a process which takes a few hours.
The most obvious place to put this process is at the start of configure. Is this considered normal and reasonable? Or is there a convention that configure should only contain the things autotools normally puts in it, and installing dependencies should be another script that the user runs first and separately? In the latter case, is there a convention regarding what that separate script should be called?
Don't install anything during configure. The scripts name is "configure" not "install-dependencies".
Write a configure check, and if llvm is missing, Give the user an explanation how to install it. If necessary provide a separate script to download llvm.
It is good practice to run configure (and make) as normal unprivileged user and not as root. So you may not even have permissions to install anything. You would have to check if "sudo" is installed, etc.
It may also happen that the system the user is installing has no network connectivity (firewall etc.), so your download will fail.
I've been stuck on a problem for two days now where the software I'm trying to install will not proceed unless I make a separate user which is non-root.
Keep in mind I'm a big linux noob and not very experienced with the OS.
I make a user called "smrtanalysis" in a group called "smrtanalysis".
I put him in the sudoers file.
I made a folder called smrtanalysis in my home/nick/ directory
I downloaded the software from the PacBio website and put the .run files into this directory I noted above.
I used chmod 777 and chown (to user smrtanalysis) on the directory
noted above, and the .run file
I logged into smrtanalysis user by su smrtanalysis, password, and typed
./smrtanalyis-2.2.0.133377.run
the file runs, but then aborts with the following error message:
We recommend running this script as a designated SMRT Analysis user
(e.g. smrtanalysis) who will own all smrtpipe jobs and daemon
processes.
Current user is 'root' (primary group: root)
Installing as 'root' is currently not supported Switch to the desired
user and restart the install. Aborting installation...
Here is the install documentation:
https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Analysis-Software-Installation-v2.2.0
It seems pretty straightforward but I can't seem to get it working. If you guys look at the install docs, you'll probably be able to tell me what I'm doing wrong.
Thanks for any help!
Regards,
Nick
change
SMRT_ROOT=/opt/smrtanalysis
on
SMRT_ROOT=/home/nick/smrtanalysis
the rest should be easy.
Be very careful installing binaries from internet, make sure you're confident in the source.
Just don't use root for that, you ran the script as root by accident.
(update: pacbio team can help from the github page at https://github.com/PacificBiosciences/SMRT-Analysis/issues as well.)
So I'd like to set up a linux machine for Haskell development with one huge caveat -- no root privs on this machine. We could of course get the admins to install GHC for us, eventually. However, in the long-term then we need to hassle them when we want to upgrade, etc. So much better to do everything in userland. Which also means that we'll want to install c libs we link to in userland as well, etc. to keep everything as hassle-free as possible.
So, the question is, how, soup-to-nuts, would I go about doing a purely userland install of GHC? The machine will have gcc, and the usual toolchain. If necessary, we can start with a typical ghc install to get the ball rolling, but it would be nice not to.
Additionally, any tips on managing an environment like this would be appreciated, especially involving how such a setup can be manageable with multiple devs/accounts.
I did this too. I created a directory ~/usr and passed --prefix=$HOME/usr to all configure scripts. Using the Haskell Platform makes this process even smoother.
You obviously need a directory that all pertinent users have at least read permission on. Say /home/foo, with subdirectories bin, lib, share, .cabal. Then ./configure --prefix=/home/foo and make && make install, and make sure that /home/foo/* is before /usr/* in everybody's PATH, LIBRARY_PATH etc. You should probably start with installing gcc and c-libs there, and when everything C is installed, install ghc.
I managed to install ghc through stack by following these instructions. It worked like a charm; the only additional thing I had to do was to install the GMP library and to add it to the LD_LIBRARY_PATH.
If you want to use stack to install ghc or ghci, follow this offical manual:
download the tar.gz file from the release link (curl/wget/even scp can upload your local file to a remote server)
extract the file with tar xvzf and enter the folder test if ./stack run properly
add
export PATH="<stack_path>:$PATH"
to ~/.bashrc
Every time you start the terminal, do source ~/.bashrc
install ghci locally
stack ghci
It will install ghci automatically and launch it.
I've written a C++ program (command line, portable code) and I'm trying to release a Linux version at the same time as the Windows version. I've written a makefile as follows:
ayane: *.cpp *.h
g++ -Wno-write-strings -oayane *.cpp
Straightforward enough so far; but I'm given to understand it's customary to have a second step, make install. So when I put the install: target in the makefile... what command should be associated with it? (If possible I'd prefer it to work on all Unix systems as well as Linux.)
Installation
A less trivial installer will copy several things into place, first insuring that the appropriate paths exists (using mkdir -p or similar). Typically something like this:
the executable goes in $INSTALL_PATH/bin
any libraries built for external consumption go in $INSTALL_PATH/lib or $INSTALL_PATH/lib/yourappname
man pages go in $INSTALL_PATH/share/man/man1 and possibly other sections if appropriate
other docs go in $INSTALL_PATH/share/yourappname
default configuration files go in $INSTALL_PATH/etc/yourappname
headers for other to link against go in $INSTALL_PATH/include/yourappname
Installation path
The INSTALL_PATH is an input to the build system, and usually defaults to /usr/local. This gives your user the flexibility to install under their $HOME without needing elevated permission.
In the simplest case just use
INSTALL_PATH?=/usr/local
at the top of the makefile. Then the user can override it by setting an environment variable in their shell.
Deinstallation
You also occasionally see make installs that build a manifest to help with de-installation. The manifest can even be written as a script to do the work.
Another approach is just to have a make uninstall that looks for the things make install places, and removes them if they exist.
In the simplest case you just copy the newly created executable into the /usr/local/bin path. Of course, it's usually more complicated than that.
Notice that most of these operations require special rights, which is why make install is usually invoked using sudo.
make install is usually the step that "installs" the binary into the correct place.
For example, when compiling Vim, make install may place it in /usr/local/bin
Not all Makefiles have a make install