I am following this tutorial. I already have .fastq files. I want to install ea-utils.
My setup is Ubuntu 18.04 bionic, via Oracle VM Virtual Box.
In terminal, I entered the command:
>>>sudo apt install ea-utils
E: Unable to locate package ea-utils
First, I installed latest Ubuntu updates via. Software Updater.
Then,
>>>sudo apt-get update
E: Some index files failed to download. They have been ignored, or old ones used instead.
Still throwing an error:
>>>sudo apt-get install ea-utils
Second command said: E: Unable to locate package ea-utils.
You cannot install it using Git-Bash. Git-Bash is not a Linux environment (apt-get is a Linux utility that can be used in a Linux environment). Git-Bash is a subset of the MSYS (or MSYS2, not sure) collection of open source tools compiled for Windows
What you can try is
build your own version of ea-utils for Windows. build guide - I will elaborate if required
check if there are any precompiled binaries for it
Expanding on building/compiling your own binaries of programs
Normally a program is written in a programming language (e.g C/C++, Java) that humans can read. These are plain text files.
That is compiled into something computers can read
This compiled file is executable on the platform which it is compiled for - ends in .exe for Windows
This executable file is distributed as a 'precompiled binary' that is copied into (usually) C:\Program Files by the installation procedure
But things change in the world of open source software
You are given the original files of code written in a programming language
You use a compiler combined with other libraries to compile it into an executable file
MinGW is a collection of tools, including the C/C++ compiler for Windows
GSL is a library that provides some other code that ea-utils depends on for the compilation of the binaries
General instructions for building
(Sorry I cannot test these. I do not use Windows any more)
Install MinGW - accepting the defaults should work fine
Install GSL - try the link that says Setup (again, accept defaults)
Unzip the file you downloaded earlier from ea-utils' GitHub
Open command prompt
cd into the unzipped folder
(based on instructions on their wiki) make
make test
Since your updated question is based on using Ubuntu 18.04 in a VM and you there is still an error, I suggest trying
sudo apt-get update
sudo apt-get install ea-utils
Commonly, software in the Linux word is distributed as "packages" - e.g ea-utils. The first command contacts Ubuntu's repositories (they serve the packages) and generates a list of all the available packages.
That should fix the error of ea-utils not being found.
Following the constant errors being thrown,
Download the .deb file 64-bit version or 32-bit version according to the virtual machine you are running. Open it inside the virtual machine, and follow the onscreen instructions.
Related
I have to work with ubuntu 14.04, but I need to use cloc 1.92. The highest cloc version via package update for Ubuntu is 1.6.
https://packages.ubuntu.com/search?keywords=cloc
I did a wget https://github.com/AlDanial/cloc/releases/download/v1.92/cloc-1.92.tar.gz to download this package to my machine, but it's not showing up in the package list when I do dpkg --list. I'm not sure how to make the cloc 1.92 folder run the same way that 1.6 does on my VM, or if it's even possible to do so.
The git page for cloc explains all related aspects, and skimming over it, in the Why use cloc? section says that the "program is self-contained, only download and run it". This program is developed in Perl 5, present in all Ubuntu distros. You can check that with the command perl --version.
Simply extract the file cloc from the tar.gz and copy it in an appropiate directory, for example /usr/local/bin, and confirm it has the proper executable rights with the command chmod a+rx /usr/local/bin/cloc.
Caveat: cloc claims to use only standard Perl modules. If your installed Perl doesn't have all needed, you will have to install them using CPAN.
Edit: See the comments by Knud Larsen for manual installing as Ubuntu mantainers do.
In this case, as the program is run by an interpreter, it wasn't needed to compile it, but in general programs/libraries in source form could to be compiled and installed independently from the apt/dkpg package management, but could need other libraries/programs to operate. The mantainer of the distro ensures this dependencies are installed together with the desired package. If we want to compile/install manually, then also we have to compile/install all requirements of the program if they aren't there already.
In other cases, the additional required software for the package could be already installed in some older versions, but it is used by other installed programs that could fail if we install new versions. That is the main problem when updating software in older distros: We need to investigate and resolve any conflicts manually.
So, the second answer is: Yes, we can update software in older versions of Ubuntu, but could be impractical to do so.
When trying to install Android Studio on my Linux Laptop, I get "Unable to Run mksdcard tool" From what I can tell from searching, this is usually caused by lacking the 32 bit compatibility libraries on 64 bit Linux, however I am running it on an ARMv7 processor, using the crouton project to use Linux on my Chromebook. I have tried install the recomended packages ending in i386, but the command line returned:
Reading Package Lists... Done
Building Dependendency Tree
Reading State information... Done
E: unable to locate package [Name of package here]
E: Couldn't find any package by Regex '[Name of package]'
Does anyone know what is causing this and how I can fix it?
I've discovered a workaround.
After a little searching, I've found that we can create executable binary of the tool for the ARMv7 platform ourselves! Whupee!
Head over to GitHub and pick up the source code, mksdcard.c. Download this to wherever you'd like, but make sure you download it as mksdcard.c and not as mksdcard.c.txt, which your browser might try to do. You can always rename the file later in case you accidentally save the filename incorrectly.
Over in your chroot environment, head to the directory where you downloaded the file.
Make sure you have the gcc compilation tools installed. Try running gcc -v in an attempt to see what version of GCC you have installed. If this doesn't work, you'll need to install GCC via sudo apt-get install gcc.
Run gcc -o mkdscard mksdcard.c. This uses GCC to compile the source code into something that can be executed. After compilation has completed, you can use ./mkscard to have Linux execute the binary file, which verifies that it works.
Navigate to your Android SDK Tools directory. This is usually ~/Downloads/Android/Sdk/tools. By running ls, you'll list the files and find the version of mksdcard that your Linux distribution doesn't understand how to run. (Running ./mksdcard on this file will confirm this.)
Backup the broken binary somewhere, then delete the copy in the tools folder. (I created a backups/ directory within the Android SDK Tools folder to move it to.)
Within the directory, use rm -r mksdcard to delete the old mksdard binary.
Finally, copy your compatible binary over to take it's place, e.g. cp ~/Downloads/mksdcard . (Copies the mksdcard binary we've created to the current directory ., the Android SDK Tools folder.)
Head back over to your Android Studio installer. In the dialogue complaining about mksdcard failing, hit Retry and the installation should continue. After it's finished, be sure to apply any updates that are recommended by the environment. Enjoy!
For newer versions eg. 3.1 C4 of Android Studio running with Ubuntu on ARM32 you will also need to place mksdcard in ~/Downloads/Android/Sdk/emulator (referencing like path from Alext T.).
we use a setup, created with install4j (we still use 5.0.11). On a new local unix machine (Linux version 3.8.13-44.1.4.el6uek.x86_64) this setup failed, the log shows:
Unpacking JRE ...
micsetup.sh: 210: micsetup.sh: bin/unpack200: not found
Preparing JRE ...
Error unpacking jar files. The architecture or bitness (32/64) of the bundled JVM might not match your machine.
Searching for this error I found this:
the program tries to run the file /bin/unpack200 which does not exist. However, the file /usr/bin/unpack200 does exist. This is due to the fact that this file is in different places depending on the architecture of the machine used - if it is 32bits, it is in one place, if it is 64bits, it is in the other. I am having this problem because the file was made to run on a 32bit architecture but I am using a 64bits machine. Therefore to fix this problem one must install 32bits libraries.
After running
sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386
our setup works.
My question: is there a way to configure the "Unix installer" in install4j to build the setup, that it works on 64 bit Linux systems like the mentioned without installing additional libraries on this system? I think not all of our customers would allow this.
Thanks in advance!
Frank
No, there is no such functionality in install4j. Bundling JREs on Linux is generally problematic.
One strategy would be to offer installers with 32-bit JRE and installers with 64-bit JREs.
I'm trying to install plone 4.3.4 on a SLES 11 SP3 64bit server via the Unified Installer. I've fullfilled all the dependencies listed in the readme.txt, but when I try to get the installer running with the command sudo ./install.sh --password=******* standalone I get the error message: which: no python2.7 in (/usr/bin:/bin:/usr/sbin:/sbin) Unable to find python2.7 on system exec path.
I find that rather strange as in the description of the unified installer it is said "The new Zope/Plone install will use its own copy of Python, and the Python installed by the Unified Installer will not replace your system's copy of Python. You may optionally use your system (or some other) Python, and the Unified Installer will use it without modifying it or your site libraries." on the Plone-Website.
So - what am I doing wrong???
I've just tried adding the parameter --build-python but had to find out that the libxml2-devel and libxslt-devel libraries that are available for SLES-11-SP-3 are sadly not up-to-date enough 2.7.6 instead of 2.7.8 and 1.1.24 instead of 1.1.26 respectively. So no joy there either. :-(
Is there any way to install the current version of plone on SLES 11 SP3 64bit?
Kate
The installer command:
./install.sh standalone --build-python --static-lxml=yes
worked perfectly for me. The installer downloaded and built the Python and libxml2/libxslt components necessary to remedy the terribly out-of-date (and vulnerable) versions included with sles11sp3.
System packages needed for the build were:
gcc-c++
make
readline-devel
libjpeg-devel
zlib-devel
patch
libopenssl-devel
libexpat-devel
man
All installed via zypper.
I'd advise not using sudo for the install. If you want to, you'll need to create the plone_daemon and plone_buildout users and the plone_group group in advance due to oddities in SUSE's adduser implementation.
Trying to compile Linux kernel for arm platform on a Ubuntu virtual machine
$make ARCH=arm CROSS_COMPILE=arm-none-linux-gnueabi-
It fails as follows
arm-none-linux-gnueabi-gcc: not found
Tried to install
$sudo apt-get install arm-none-linux-gnueabi-gcc
E: unable to locate package arm-none-linux-gnueabi-gcc
Where to find the correct package? how to include it in the system? (I found a couple of links on line that didn't work for me). It would be great if you could provide a correct solution or reference.
The Ubuntu package names are gcc-arm-linux-gnueabi/gcc-arm-linux-gnueabihf.
For building the kernel, which one you use does not make much difference. For building anything else, "gnueabihf" is the hard-float version. For any modern ARM processor (this statement excludes the Raspberry PI), this is the one you would want.
Download arm-2013.05-24-arm-none-linux-gnueabi-i686-pc-linux-gnu.tar.bz2 from https://sourcery.mentor.com/GNUToolchain/
or https://sourcery.mentor.com/sgpp/lite/arm/portal/subscription?#template=lite
Get correct version of the arm-none-linux-gnueabi toolchain (i.e. targetting GNU/Linux rather than EABI).
untar it
tar xvf arm-2013.05-24-arm-none-linux-gnueabi-i686-pc-linux-gnu.tar.bz2
open bashrc
vi .bashrc
at the end add below comand
export PATH=$PATH:{path to toolchain}arm-2013.05/bin
e.g export PATH=$PATH:/home/vinay/under_linux/arm-2013.05/bin
save it and quit the terminal.
then you can cross-compile without everytime export.
Also take of correct toolchain there are two toolchain available choose according to your requirement.
Cross compile error "arm-none-eabi-g++ cannot find entry symbol"