I am installing cufflinks on my Mac OS X, and here is the instruction:
http://cufflinks.cbcb.umd.edu/tutorial.html
Under Installing the SAM tools I follow the instructions below
Download the SAM tools
Unpack the SAM tools tarball and cd to the SAM tools source directory.
Build the SAM tools by typing make at the command line.
Choose a directory into which you wish to copy the SAM tools binary, the included library libbam.a, and the library headers. A common choice is /usr/local/.
Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/)
Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
Copy the samtools binary to some directory in your PATH.
I've done the fist 7 steps, but I am not sure how to proceed with the last step (#8): should I use the command:
sudo cp -a samtools-0.1.18 /usr/local/
or into some other directories? What does the PATH in step 8 indicate? Thanks!
To answer your question I will go over some basic linux knowledge that has helped me understand binaries and their locations.
In linux, you can run a binary by typing in a complete path to the binary and the binary will run. For example, if I have a binary named foo in /usr/local/bin, I would run the command /usr/local/bin/foo and the foo binary would be run.
The purpose of the PATH is a shortcut so that you don't need to type in the complete path to the binary, just the name of the binary. PATH is a variable that contains all of the directories that have binaries that you want to have the shortcut apply to. So, referring to the previous example, if /usr/local/bin is in my PATH variable, then I could just run foo.
So, to answer your question, you can tell which directories that are in your PATH by running the command echo $PATH and if one of the directories is where your samtools binaries are, your good!! If not, you can move your samtools binaries to one of those directories so that you don't have to put the full path everytime you want to run the binaries.
Related
I’m not root for the linux server,
so I choose to install softwares in my $HOME/local/bin, I already added the $HOME/local/bin directory to the PATH environment variable, wrote in my .bashrc.
Some softwares install this way like:
tar xvzf ncurses-5.9.tar.gz
cd ncurses-5.9
./configure --prefix=$HOME/local
make
make install
cd ..
So it will directly install in my $HOME/local/bin.
But for some softwares, after download like sbt-1.2.1.zip (based on java), and decompression, shows just a file fold sbt, it contains three foldsbin conf lib, and in its bin, contains one executable file named sbt and java9-rt-export.jar sbt-launch-lib.bash sbt-launch.jar sbt.bat.
Here I wonder:
I should just soft link this executable sbt file path under my $HOME/local/bin, then source my .bashrc?
Or, after decompression, add one line in my .bashrc export PATH="downloadpath/sbt/bin:$PATH"?
Since just one executable downloadpath/sbt/bin, so I'm not sure it is right to add whole bin fold path, if software's bin fold contains executable files (one or many), I think this situation is more convenient for just add it's bin in .bashrc, but even so, I'm not sure its right?
I'm not familiar with installation software, now I usually know way
but not why. Here I shows two ways (more ways not be showed here) to
install, executable file always be written in bin or src? But some
softwares no bin just src but no executable files in it...
Slurm also can use modules to install software, conda also other way, but I want to
confirm these traditional ways I mentioned (that two) still can be
used on slurm or conda?
However, any suggestion even one aspect's reminding will be grateful!
For precompiled software, or, in general, software that does not offer configure scripts or (C)make files, it is ofter better to leave them in their target directory and adapt the *PATH (PATH to binaries, but also LD_LIBRARY_PATH, LIBRARY_PATH to libraries and CPATH to include files and MANPATH to the man page) environment variables.
The reason is that the software might be configured to read files with hardcoded paths, relative to the position of the executable, such as libraries, etc.
In your case, you might also need to setup the CLASSPATH env variable to the directory with the jar files.
To ease software installation, you can use tools such as easybuild that can help, and even create user modules just like the system module installed by the system administrators.
There is something wrong in my opinion with your setup. If you don`t have root account on your server, is not better to test what you have to test, in a more safe environment - for example a vm/container on your developement machine ?
However, in your situation maybe it can be better to start sbt by using a separate bash script than modifying your .bashrc
I just installed Cmake from git clone wget http://www.cmake.org/files/v2.8/cmake-2.8.3.tar.gz in a new folder on a Linux server. The compilation worked but cmake command is not recognized from other paths. Should I copy the entire contents of cmake-2.8.0 folder to usr/local/bin? Or is the contents of bin folder that need to be copied?
Thanks
On Linux and other Unix-based systems, a common arrangement is to install packages to /opt and add relevant entries to the PATH environment variable to make them available. This is intended for packages not provided by the native package manager or distribution. By choosing an appropriate directory structure, this can be done in a way which also allows different versions to be installed simultaneously and the user can pick which one they want by adding the relevant directory to the PATH.
For the specific case of CMake asked about in the question, you can use a directory structure like /opt/cmake/<version> and then add the relevant /opt/cmake/<version>/bin directory to your PATH (e.g. /opt/cmake/3.8.2/bin for the 3.8.2 CMake release). You can even just download the official pre-built CMake tarballs, unpack them and move the top level directory into the /opt/cmake area as the particular version you downloaded. I've used this successfully on Linux, MacOS and Solaris, as I'm sure have many others.
Note that once you've run CMake on a particular source tree, the cmake executable doesn't need to be on the PATH any more. If cmake needs to be re-run, the build will do so itself and it records the full path to the cmake executable in its own cache, so the PATH isn't even consulted (this is essential in ensuring the same version of CMake continues to be used for all builds regardless of the PATH, since PATH can change between login sessions, etc.). You would only need cmake on your PATH if you intend to invoke cmake manually or for the first time you run it on a source tree, but in both of these cases you can always just use the full path to the cmake executable if you preferred.
I should also add that the entire set of files provided in the CMake package are required, not just the bin directory. CMake makes extensive use of files in its other directories, such as the various modules it comes with. If you are building CMake from source, you may want to build the package target so you get a relocatable tarball or similar which will contain everything that should be included when you provide a CMake package on your system.
After the build, use 'sudo make install'. This will make sure the correct libraries and binaries are copied to their proper places.
Usually this will install the binary to /usr/local/bin.
Make sure the PATH variable has this included.
sudo make install did not copy to /usr/local/bin/ for some reason, so I copied the content of CMAKE /bin. to usr/local/bin an it worked.
cp –a bin/. /usr/local/bin/
I am little confused on how to create a complete binary package using rpmbuild from a project I just created (already compiled binary).
my current project contain similar format as this user (Packaging proprietary software for Linux)
Where I have
foo (binary)
data
libs
foo.sh
libs will contain all the shared libraries the project requires, and foo.sh is a script that sets LD_LIBRARY_PATH to include libs. Therefore, the user will execute foo.sh and the program should start.
I am looking at the tutorial from this site (rpm tutorial)
I understand to create a rpm I create a build area use rpmdev-setuptree
I can create a spec file use cd ~/rpmbuild/SPECS; rpmdev-newspec foo and if I got a good SOURCES folder I can build it with rpmbuild -ba foo.spec
But I have no idea how to setup the SOURCES directory. The tutorial stated (here) that I should create a tarball and place all my source file in it and put in SOURCE directory. What would be the source file in my case?
You are trying to create a RPM from binary files you have already? In that case, you can just leave the whole building stuff out of the SPEC file, and you need a SOURCE directory to keep the bundles you've got, the %prep step described below will take them from here.
In a binary package I built a while back from zip files, I did:
Heading, with name, version, description written by me/cribbed from the originals
Sources: The original places to download the Linux packages, official documentation, ...
%prep: Just unpack the different pieces, delete some redundant files, ...
%build: Nothing to do
%install: Create the relevant directories under $RPM_BUILD_ROOT by hand, copy files there by install, copy/create configuration files, ...
%clean: Blow away $RPM_BUILD_ROOT
%files: An exhaustive list of all files installed.
This required a few iterations to get right. Afterwards I followed the upstream package by rebuilding my RPM (conveniently I had everything packaged up in a SRPM, where the Source part was kind of a misnomer...)
My question regards the GNU build system, namely, the configure, make, make install build system. My question regards "make install" specifically. Let's say there is a bin directory a man directory etc. where I install all of my binaries and man pages. What happens if there is a name clash. For example what if there were a binary called program and then another package also has a binary called program? When I do make install on the second program will it overwrite the first?
The behavior of the "make install" command varies, but the short answer is essentially correct. "make install" typically copies files from the build directory to some system directories, and those files would overwrite files that already existed in the destination directories.
In the process of building an RPM package, I have to specify the BuildRoot and later will be used in %install which invovles $RPM_BUILD_ROOT. I always think that $RPM_BUILD_ROOT is the fake installation for RPM to perform packaging. Then, at install time using the RPM package, it will install into actual location. For example:
$RPM_BUILD_ROOT/usr/bin
I thought that $RPM_BUILD_ROOT is for the packaging process only, and in some ways RPM can distinguish the $RPM_BUILD_ROOT and the actual install location when the user performs "rpm -ivh package.rpm" will be /usr/bin.
But recently upon reading some documents, it is suggested that $RPM_BUILD_ROOT is the actual location which will be installed, and the $RPM_BUILD_ROOT is specified by user with the setting of environment variable $RPM_BUILD_ROOT in order to let the users install the package in their desire locations. Otherwise, $RPM_BUILD_ROOT will be null and it will install into the default location. In the above case, it is /usr/bin . Thus, $RPM_BUILD_ROOT is not just for packaging or "fake installation" process, but is a way for user to define install location, similar to select folder location in Windows.
I don't know my thinking is correct or not. Can someone please verify? Thanks in advance.
$RPM_BUILD_ROOT (or the equivalent %{buildroot} SPEC file macro) always holds the directory under which RPM will look for any files to package. The RPM scripts (e.g. the script that compresses the manual pages) will also use that value to know where to look for the files that were just installed. Normally, this value will be non-empty and contain a location away from the system directories - usually somewhere under /tmp or /var/tmp.
The author of the SPEC file is expected to make sure that make install (or whatever installer the software in question is using) will place any files under $RPM_BUILD_ROOT, with the same hierarchy that should be used when the software is finally installed. E.g. to have RPM install ls in /bin/ls, the %install SPEC file section should make sure that ls is placed in $RPM_BUILD_ROOT/bin/ls.
The author of the SPEC file is also expected to use the BuildRoot: tag to specify a proper location. Alternatively, the build system could have an rpmrc RPM configuration file with a proper entry. In any case the build root should be set, so that:
Normal users will be able to build the source package.
Should the superuser ever build the source package, the build process will not clobber any system files, unless the superuser installs the resulting binary package. And yes, there may be a good reason to build some packages as root - for example, running the full glibc testsuite requires root privileges for some tests.
That said, RPM can and will build a package with an empty build root variable. In that case both the build install and the final destination locations will coincide. A potential call to e.g. make install will use the default locations, thus clobbering the system files under e.g. /usr/lib if run with sufficient privileges. Additionally, having /usr/bin/* in your %files section will happily pull the whole contents of the build host /usr/bin/ directory into your binary package.
Bottom line:
Never use an empty build root.
Do not build packages as root unless there is absolutely no other way.
the file ~/.rpmmacros defines the paths per user:
%_topdir %(echo $HOME)/rpmbuild
%_tmppath %{_topdir}/tmp
and one can also define them with rpmbuild command line parameters:
rpmbuild --define '_topdir /home/username/rpmbuild'